How to structure a Xcode project with Frameworks, Extensions and CocoaPods

Question

NB: Here is a more abstract and simplified sub-set of this question.

With the addition of Touch Frameworks, Extensions and the Apple Watch Xcode 6 projects and

Answer 1

More of a comment than an answer, but I don't have enough reputation for it: Have you tried using the cocoapods xcode plugin? I use it and it structures the pods on its own, so I don't even have to worry about it.