I don't believe that it's currently possible to configure Back In Time to save the backups anywhere other than a folder on the filesystem (Deja Dup is able to back up to other places, as you know, such as Ubuntu One).
(warning: super techie stuff ahead)
It might be possible to back up to Ubuntu One with Back In Time by mounting your Ubuntu One storage as a folder -- doing this would require someone writing something like a fuse filesystem or mountable server using the Ubuntu One files APIs, which as far as I'm aware no-one's done, and I personally would be very worried about trusting my backups to such a setup -- what happens if your broadband dies halfway through a backup taking place? Without some cooperation from the backup tool itself (B.I.T. in this case) you'd need to be very careful. If the Back In Time development team are interested in making Ubuntu One a backup target then I (as head of U1's app developer programme) am more than happy to chat to them about how they might go about it! Failing that, though, I'd stick with Deja Dup for now to back up to Ubuntu One if I were you :)