I wish there was better documentation for this for Xcode 5 but I couldn\'t find anything decent describing best practices for working with workspaces, so..
In a workspac
Consider migrating to CocoaPods.
Not only it will fix your build problems, but with a project as complex as you describe it will ease your life when updating/adding/removing frameworks, changing target system version and resolving dependencies and conflicts.
Also your workspace will likely become only two projects.