When it comes to animations, personally I recommend rendering out your passes/layers as image sequences. That way I don’t have to re-render 3D + composition if Blender crashes.
There’s nothing wrong with compositing them in the same scene file as your 3D stuff, but sometimes I choose to start with a fresh .blend file.
I’m almost certain most artists work based on their preference, not all the exact same “best” workflow.
I hope that’s helpful. You can see in the Piero course how I generally work when rendering and compositing animation: https://cgcookie.com/course/short-film-character-production/
