The RD6000 supports running the ailerons on two channels. If it works like Futaba you have to enable flaperons even if you don't plan to use them. If you use the Y harness the orientation of the servo arms should be so both are pointing toward the fuselage, or both pointing toward the wing tips. The manual for the plane should tell you which way to point them. Even if you run two channels the orientation of the servo arms will not change.

Advantage to using two channels - you can use flaperons if you want
Disadvantage - takes longer to set up the controls because you have to set servo travel end points on two channels rather than one

You'll need your transmitter manual to be able to set up two channels. On Futaba it is not hard to do. I have to think Airtronics also makes it pretty easy.