With great effort, I managed to build one of my Apple Watch capable apps with both the WatchKit 1 targets for running on iOS 8.4 and the WatchOS 2 targets for running on iOS 9. I can debug the app on a physical iPhone and Apple Watch running 8.4 as well as debug on the 9.0 simulators for iPhone and Watch.
However, when I archive the project, ValidateEmbeddedBinary throws the error: WatchKit Extension doesn't contain any WatchKit apps. Verify that the value of WKWatchKitApp in your WatchKit App's Info.plist is set to YES.
I dug down into the derived data build artifacts, drilling into the packages and it clearly shows the Info.plist for the WatchKit app having WKWatchKitApp set correctly. I have checked that each of the 5 target Info.plist are being built from the correct folders.
I have a shell of a dual watchkit app that archives just fine. Comparing the 5 plists in the shell to my fulll app shows no differences. Same issue whether running Xcode 7 GM or beta 6.
Adding WKWatchKitApp to the WK1 extension's Plist did not make any difference. Removing WKWatchKitApp from the WatchOS2 extension also did not help. It's not clear whether this setting is needed in both targets
I filed bug 226452134 with Apple. Since they haven't looked at another related bug report regarding dual build watchkits that I filed over 3 weeks ago, I don't expect any resolution to this one soon.