Just a thought here.
I wonder what post editing software you are using, and does it have a 'chromokeying' function.
If so, that can be very handy when working with large projects.
Not so much to help keep things in order, but to give your PC less work.
At the moment i'm working on something that is pretty large. My biggest problem is wheteher my computer can handle rendering some scenes, with multiple characters.
One way i've found to lessen the load is by rendering the scene in more than 1 take, with a greenscreen background. (for chromokeying).
eg: 2 people walking through park, with other characters doing things all around them.
1) render the 2 characters walking.
2) render the other characters doing their thing.
3)render background, and anything else that needs adding
4) overlap the scenes in a video editing program, so that all is visible at the same time. (chromokeying).
Its not right for all big scenes, but i find that when i can use this method, it makes some scenes possible, which otherwise my computer would really struggle with.
Just a thought.