Did you put the control horn on opposite sides of the servo? Or are you just in the planning phase?
with ailerons you want the control horn hooked to the servo arm through the push rod on opposite sides
of the servo. But for flaps you want the control horn through the push rod to the servo arm on the same side of
servo. So if you're having different travel (one up the other down) a simple fix would be to move the control horn over, then you can have the servo arm on the same side of the srvo