A few quick things:
1. Probably worth mentioning that the documentation doesn't currently point out that you need to setup two ipad resolutions if you want to prevent default fallback: 1024x768, and 2048x1536.
2. It would be really nice if this weren't actually necessary :)
3. Here's a tip for others who don't want to manually copy all of your buttons: if you put unity's inspector in "Debug" mode (right click on the top of the inspector tab) and select the BrassMonkey Prefab and find the "BMControlScheme" - you can merely change the Size property on the Resolutions array, and it will duplicate the default one, buttons and all. From there hopefully it's just tweaking...
-Aaron.