You have to decide ahead of time with the 9C whether you want aileron differential or the flaperons option. It will matter whether you choose channel 6 or 7. If you don't plan on using either - you still have to tell the transmitter which plug the left servo is in or it will only operate the right aileron.

A "Y" in channel 1 works fine if you just want simple ailerons.

I have an older 9C and it is a great transmitter. I highly recommend Harry Higley's pamphlet: "Radio Programming the Futaba 9C" as it goes above and beyond the manual.