Hi Rick,
Not sure which six channel Futaba radio you have but you may be able to asign the flaps to a choice of controls. If not your proposal with the "Y lead" should work but you will have to set up the flap throw mechanicially. You will also probably need to set up the aileron servos so that you connect to opposite sides of each servo control arm.
Make certain that your model memory has all settings at the factory defaults (sub trim, end points etc) and set up everything to the throw settings determined by the templates that came with the kit. You don't need more than the recommended throws although the CofG is very conservative
.
Cheers,
Colin