Got it working. After creating a SB project, instead of trying to move the project file outside of the .spritebuilder folder into my already existing project, I just deleted the Xcode project Spritebuilder automatically generates for you. Then I took the .spritebuilder folder and put it inside my Xcode project folder. I guess the Spritebuilder document needs to live inside of the .spritebuilder folder?
I set it up so my Xcode project only keeps references to the published .ccbi, and the resources it needs, but the SB project I just have live inside the Xcode projects directory, instead of the other way around. Seems like that's the only way to add a SB project to an existing Xcode proj right now.
Anyway, looking forward to finally checking out v3/SB.