First off, you have to get the flaps set up mechanically, first. With both transmitter and receiver turned on, put the 3-position flap switch in the center position. The servo arms should be at 90-degrees to the servo case. Remove and replace the servo arm to get it at that 90-degree positioin. You may need to turn the output arms 180-degrees to get the servo arm exactly centered.

Now, mechanically adjust the pushrods so that the flaps are at their 1/2 down position.

Now move the flap switch to the flaps stowed position. Adjust that endpoint so that the flaps are in trail with the wing.

Move the switch to the full flaps-down position. Adjust that endpoint to the amount of deflection required.

You will have to adjust the endpoints as needed so that both flaps move together.