I have the same issue.
I just installed my AppRadio 3 w/ iPhone 5 and all required cables + Microbypass. When I go to the AppMode and I click the Waze icon from the AppRadio screen, Waze open on the iPhone and get mirrored on the AppRadio, meaning it only duplicate my iPhone screen on the AppRadio. I can't use the HU screen to navigate...
From what I've read and saw on Youtube, I should be able to control Waze from the AppRadio. Anyone knows how I can resolve this issue?
Thanks !