RE: Flapron and aileron diff
Flaps are usually controlled by a knob that is turned and the flaps move proportionately. It sounds like you are using a switch for flaps on or off.
If possible try using the channel that has the knob on your transmitter to mix with ailerons for "flapperons". When you turn the knob the ailerons should move accordingly.
Also make sure your end points settings are correct.
Hope this helps. It is difficult for me to understand exactly what your situation is.
Wings