Another contributed explanation

The next scene sees Abe on the roof of a building, he's looking out over the park bench where Aaron is sitting. He's in the power position denoted by him looking down over the world. He knows how this day will pan out. This is the first time Abe has returned from the future. Let's call him Abe_1. As we'll see in a few seconds, there are now 2 Abes in this timeline.
The other thing to notice here is the sound of the ocean and waves as Abe enters the roof. This is an audio cue signifying time travel. We'll learn this later when Aaron and Abe discuss the dream they each experience whilst in The Box.
Abe_1 approaches Aaron who's sitting on the bench with a radio earpiece in his ear. He's listening to NCAA basketball. In the next few scenes Aaron continues to wear this earpiece.
I took note of the neckties they're wearing to ensure they stayed consistent and we didn't switch from Abe_1 back to Abe at any point.
Abe wants Aaron to ditch work and go visit Bradshaw, an engineer. On the way out of the office, they split up and Aaron goes to inform Will that a meeting has been cancelled. We learn later that Will is Rachel's ex-boyfriend's cousin.
In the next few scenes, Aaron learns that a protein has grown on their weeble. Normally this protein takes a long time to grow, theirs has grown in a short time.
The entire time, Aaron is wearing his radio earpiece in his left ear, the same ear which will later begin bleeding.
It's 2:05pm when Abe_1 describes to Aaron what's happening to their Weeble in the small box.
it's experiencing the same second, over and over again.
We also learn that the original purpose of The Box was to "degrade gravity". This is not important except that when this audio of Abe talking is played, it sounds distant like it might be on Aaron's earpiece. This hints, as we'll learn later, that this might not be Aaron but it might be an Aaron from the future!!! I don't buy this though as Aaron's writing (on the pad) is normal. He's not writing like a baby (we learn later that time travel degrades your handwriting).
Time between the A and B ends of The Box represents 1 minute. If the Weeble enters at the A end spends 1 minute realtime in The Box and leaves at the A end, it'll experience an even number of minutes, i.e. 1334 minutes in the movie. If it enters at the A end, spends 1 minute in The Box and leaves at the B end it'll experience an odd number of minutes in The Box. i.e. 1347 minutes in the movie.
They've accidentally discovered time travel here and the description is somewhat reminiscent of some of the Quantum mechanics books I've come across.
So in the next few scenes, they decide to build a bigger Box so that they can go in and control which end they get out of The Box. Abe_1 plants this idea in Aaron's mind, a classic "time-travel movie paradox". So far this is typical Marty-McFly time travel stuff. The basketball scene in the yard ends with Aaron saying "we're going to have to move it", Abe_1 responds "We will".
Next up they're sitting on the truck bed beside the storage facility. Abe_1 continues to plant the idea of how the machine will be built into Aaron's mind.
When Aaron says "You know what we could use", Abe_1 switches from pretending like he's Abe into the mode of being Abe_1. He knows Aaron is about to see regular Abe  enter the facility and he must brace Aaron for what he's about to see.
Aaron is NOT wearing an earpiece at this point. Again, this indicates he's regular Aaron, and not an Aaron from the future.
Aaron sees Abe enter the facility. The camera switches to a view of Abe_1 and Aaron watching the facility. This shot hints that they might be being watched by another version of themselves but I think this is another red-herring.
Abe_1 and Aaron enter the facility and wait until Abe has entered The Box. They sit beside The Box in a very poignant moment.
Aaron says "What did you do all day, the first time through", indicating that this is not Abe_1's first time coming back and hence he's technically not Abe_1, he might be really Abe_n. We can't know what revision he is though and it's not important.
Aaron wonders what he did that day and it's interesting that Abe_1 doesn't know either although after thinking about this, I don't think this matters.
During this conversation, the phone rings and Abe_1 answers. It's Rachel. The fact that the phone rings and he answers is OK as since Abe has entered The Box, then there's no loop.
Also, at this point, there's only 1 box in the storage room. I assume though that since this is not Abe_1's first time through, that he must have built the failsafe device and it must already be running in it's own storage room.
FAILSAFE SAVE POINT!!!
In the next few days they build a second box (Aaron still doesn't know about the failsafe) and then prepare for them both to make a trip.
So The Boxes work like this. The second you start The Box (8:45am in this scene) is the time you'll exit, regardless of when you enter. You must shut The Box off before entering and you must enter before The Box fully winds down. You must also exit The Box right when it's started, hence the stopwatches and alarms. If you exit too soon, you might go into a coma (I assume). To avoid being at The Box when your double exits, they use timers to give themselves time to leave. The time is set for 15mins and started at 8:30am. When 15mins is up, The Box starts up.
Abe_1 says "There are always leaks". Not sure what this means but it might be a hint of things to come. Fractures in their relationship and trust.
They drive to Russelfield to check into a hotel. This is to avoid affecting the world whilst they're traveling back in time. In the hotel they play Scrabble and Aaron tries to use all his letters and place a word that does not exist "Evacipate".
On the way back to the storage facility, for their first trip, Abe_1 checks the lock on a storage locker. Then moves to the real storage locker. Is this the locker holding the failsafe device? We learn later that the failsafe is in a locker upstairs from this one. Another diversion from Shane.
Right before Aaron enters The Box for the first time, he reads a piece of paper. It roughly reads:
"Rules to Follow to Evade Causality Paradoxes or Generally Screwing Your Life Up"
1. Do not disturb The Box after you exit as you or your double is in it.
2. When re-experiencing time, stay away from your double until he/she has started his/her journey backwards.
3. Worry about yourself first. Now is the only moment that has to make sense.
They enter The Box and we hear faint hint of waves in the distance along with the hum of The Boxes.
They get out just as the machines are starting up, at 8:50am. Abe says he left the machine on since he or his double or "someone" was on the way back. Who's "someone"?, why would he say that? Did he tell Granger about The Boxes in order to get funding and did he have Mr Granger try one out?
They decide to trade some stock and make some money using mid-cap funds to avoid getting caught. Later that day they drive back to the facility, park and watch their double's going into the facility, just for kicks.
In the next scene, Aaron's wife Kara complains about rats in their attic. Aaron claims they are birds and to leave them alone. He must know at this point that the noise in the attic is actually his drugged double. If he hadn't been up in the attic he'd be supportive of getting the exterminator. I mean, who wants rats? This means Aaron at this point MUST be an Aaron from the future.
Aaron also suggests using the time machine to punch out Platt. Another Paradox! He wants to go to see Platt, punch him and then enter The Box, go back in time, go visit his double before punching him and then convince him not to do it. The problem with this is even if he manages to convince himself not to punch Platt, he must also convince his double to go enter The Box. It's basically an experiment to see what would happen. He'd have punched out Platt and yet not punched him out. There's no point other than curiosity and the idea has been planted by an Aaron from the future.
The gas-pump scene is when Aaron breaks down a little to Abe, he's talking about life, the way things have worked out, what if this is your first or second time through etc. One of the great lines in the movie: "What's worse? Thinking you're paranoid or knowing you should be?". I presume he's talking like this as he's secretly from the future.
Abe is beginning to suspect Aaron.
In the next scene, they've been back through obviously, they're trading stocks again and discussing telling Aaron's wife. They decide to not tell Roger and Phillip.
After a few more trips through together and a discussion about Aaron's dream, Aaron begins bleeding, presumably from excessive time travel or being awake for so long. He's been traveling through with Abe and also on his own.
In the next scene, Abe is in the garage when Roger and Philip come in. Roger thanks Abe for the present. We learn later on that Abe bought Roger a vinyl record of the "Best of Bread". Roger states "you guys make fun, but there's a difference", implying the superior quality of records over CDs. Roger refers to Aaron as "Hero". Abe doesn't notice at first but then realizes. What follows is an explanation of the events of Roger's birthday party when Aaron rushed Rachel's ex-boyfriend.
NOTE: Abe wasn't at the party in this timeline, so he needs Roger to explain the "hero" incident.
Abe didn't know about the party as Aaron didn't tell him. The birthday party was on the night when Abe_1 first explained everything to Aaron. Abe_1 and Aaron did NOT go to the party originally. This re-inforces the idea above that Aaron is an Aaron from the future. I'm going to refer to him now as Aaron_x as I'm not sure which revision he is. We learn later that it took more than 1 try to get the Birthday party incident correct. We also learn that even when Aaron_x wasn't there noone was hurt. Aaron still desires praise so he figures he'll reverse engineer it by changing how the party plays out.
In the waterfall/garden scene, Aaron_x says "things are different right now". He's referring to the power to revise that they now have.
Aaron_x and Abe are in the hotel room when Aaron_x's cell goes off. He answers the phone and it's Kara.
They go back. There's a great line in next scene. They're sitting in a room, Abe is meticulously slicing a cupcake and Aaron_x says "Are you hungry? I haven't eaten since later on today". It's also interesting that although Abe and Aaron_x are watching a sports game, they both know the outcome. They're clearly not following the original rules of switching everything off and unplugging stuff.
They go for food and are walking down the street at the same time when the original phone call was placed by Kara. Aaron_x took the phone with him (by mistake) and it goes off again. Thus, the question, did it really go off in the hotel room? And did he answer it? Another paradox.
Next things get sketchy. Abe is woken by a car alarm. He decides to do an experiment, to go back in time with Aaron_x and prevent himself being woken by preventing the alarm going off. Thus creating another paradox.
He tries to tempt Aaron_x into going along with this by offering him the Platt face-punch. Abe also reveals he's been turning The Boxes on at 5pm. This is bad as he's didn't tell Aaron_x and he's potentially using the boxes without Aaron_x's knowledge.
They leave and notice Granger is following them. They call Granger's house, he's there! This means that Granger has gone back in time and the future Granger (Granger_1) is in the car. They give chase and Granger_1 falls in to a coma when Abe gets near him.
Something has happened between Abe and Granger. They're asking "what did he change?" They might be referring to Granger here or the might even be referring to a revision of Abe!. Abe decides he must use the failsafe machine. The failsafe's been running for 3 days 22hours when Abe uses it.
Let's now call Abe from the future Abe_2. The next few scenes are pivotal.
Abe_2 goes back and gases Abe_1 whilst Abe_1 is asleep!!! Abe_2 then attempts to meet Aaron on the parkbench as Abe_1 originally did. He passes out as he's just spent 4 days in The Box.
Aaron is no a revision from the future. We know this as Aaron is listening to a tape and responding according to the tape.
"At this point there would have been some...discussion".
Abe want to know "how". The how here is how everything has happened, here's my take:
After originally meeting Abe_1 on the parkbench, Aaron saw the manifest and found out about Abe's failsafe. Aaron decided to take a box with him through the other box thus creating 4 boxes and his own failsafe. In order to get back to a point before the parkbench, he must have used the failsafe, hence breaking the original assumption that they are single use only.
At this point he had lost trust in Abe and was operating alone.
Aaron then went into a loop of trying to be a hero at the birthday party. He recorded the days events just in case his first attempt at the party failed, attended the party by himself (without Abe), tried to rush the ex-boyfriend but things went wrong. So he had to try again.
In order to try again, it meant going back to that morning, then playing things out just perfect so that the party would still have a scuffle. He'd use the audio tape for this.
The problem was that the party was on the same day that Aaron originally met Abe at the bench. It wasn't a day when Aaron had been stuck in a hotel as with the other days. So Aaron had to somehow take his own place that day.
The second time through, he meets the "Hooded Aaron" who is the one who has used the failsafe. This failsafe was setup when Aaron took a box back through the other box (after finding Abe's failsafe).
The hooded Aaron has already drugged his double and put him in the attic. We know he came through one of the failsafes as his beard has a few days growth on it. Hooded Aaron leaves as his whole intent was to record the days events and become the hero at the party.
So things play out from here. Abe is now Abe_2 from a few days in the future and Abe_1 has been gassed and is stuffed in a room adjoining a bathroom. Abe_2 doesn't know that Aaron0 is in the attic!
Original Aaron0 is up in the attic.
Aaron in the white-shirt has been looping through this day for a while, trying to get the hero thing to work. He knows Aaron is in the attic and hence tells Kara that the rats in the attic are really birds.
There's also hooded shirt revision of Aaron who has just left! I guess he's gone off somewhere.
They both continue repeating this day until it comes off just fine. We even see Abe with his own recording at the party. The best part is that nothing happened originally when they weren't there, or maybe it did, we don't know.
In the end, we see a version of Aaron talking to Abe_2 at the airport. Abe2 has found out about Aaron in the attic. He's pissed. He decides to send Aaron on his way and stay and watch over Aaron and Abe to ensure they never build these boxes.
We later see either Aaron or hooded Aaron in France building a room-sized box.

I'm not sure this explanation works, but it seems the movie is left open to interpretation. It's a puzzle.