flyboy,
The Futaba website has FAQ's about their transmitters. The page on the 9C has a question, and response, as to setting up 4 ailerons on 4 different channels. It is specific to the 9C, but probably adaptable to other Tx.
I am working on a Bipe also and went loking for the same information one time. I wanted to set up the lower ailerons (only) as flaperons and the upper ailerons as ailerons only. Don't think that can be done, but I don't really think a bipe (Waco) will need flaps, either.
http://www.futaba-rc.com/faq/faq-9c-q682.html