You need to create two new AppIDs in the Developer Portal with the correct bundle identifier for your Watchkit app and Watchkit extension. The bundle identifier has to extend the main apps identifier, so if your app is com.myapp
it should be com.myapp.watchkitextension
and com.myapp.watchkitapp
You also need to create the related Provisioning Profiles for the AppIDs, one for the extension and one for the app.
Add required add ons (like Keychain) if you are using them in your Watch app.
All in all you will need six PPs, 3 for development, 3 for archiving/store. With Xcode 6.3 team provisioning for development stopped working (for me)
Next goto Xcode > Preferences > Accounts > YOUR_ACCOUNT > View Details ..., CTRL+Click one of the Profiles and open in Finder. Move all Profiles to Trash, then refresh the Profiles.
In your targets make sure you have the correct Team set for your main App target, the Watchkit extension target and the Watchkit App target, also make sure you have the right Provisioning Profiles assigned to main App target and the Watchkit extension target (Watchkit app Provisioning Profile can not be set but will be assigned automatically Edit: With Xcode 6.3 it can has to be set).
To be sure all is fine clean build folder: In Xcode hold command and do Product > Clean build folders ...
Now you are ready to archive.
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