Ah, unfortunately I haven't tinkered around with toggling backgrounds just yet, however I know it can be done. Mewtwo2000 has that what is love stage that toggles between a good number of backgrounds to make the animation work (albeit all 2-D).
On a side note, any idea when those Gerudo's are going to be ready?

I've been keeping track of your project, because from the preview I saw they look pretty epic!
