Well actually I did have the characters in seperate compositions. I had everything worked out before hand with the timing so that I could just go back and forth between the comps and fix things if needed. I had the seperate comps in a final one where I could see how they were interacting together. In the final I only had 4 layers, ter and the box, seco, the background and the music.
The many layers came in with the rigs themselves, because I wanted the most control out of them as possible. It wasnt too bad though, I would say about 15 layers for seco, and ter had about 18.