Jim , I think it really depends on your work flow.
1. If you are doing a lot of dynamic link of clips from PrP to AE
a. A Global AE project file with lots of comps seems the only way to do it since it avoids the pitfalls of several same named projects and comps screwing things on your timeline up.
2. If you just build in AE then render out files to be imported to PrP, I have a separate AE project for each thing I build. And organized into folders that make identification easy when rebuilding is needed.
Whatever fits your creative style.
Tom Daigon
Avid DS / PrP / After Effects Editor
http://www.hdshotsandcuts.com
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