All VC.h files are unchecked by default in Xcode 6.1's Target Membership under the file inspector yet all VC.m files are checked. Am I supposed to send my Xcode project to App store with VC.h target memberships unchecked or am I supposed to check those?
That is correct behavior, only .m or .mm files should have target memberships.
You can find the Target attached source files in, Project Settings > Target > Build Phases > Compile Sources
If your viewcontroller name is there, it means it is attached to Target output.
Hope this helps.