We're not sure what you mean when you mention that you have difficulty getting the flaperons to operate "correctly". Do you mean that the flaperon function's not operating correctly?

If you're using two aileron servos and not going to use the ailerons a flaps, then you do have to slave channel 6 to channel 1.

If you want to use the ailerons as flaps, too, then you use the flaperon function.

You don't do both.