What will the main_edit.blend be used for? Is it the blend file that will act as a Video Sequence Editor and point to the comp.blend, where the comp.blend combines the layout.blend and anim.blend?
It should just link in all the most recent rendered outputs. That means it will probably start with the layout or animatic files and eventually be replaced by the openGL renders of the animation, and then finally the actual rendered images.
So it will basically be the file that you render out to be your final full movie.