First, set the airplane to the 2 Aileron 1 Flap wing type. Then assign the flap channel you're using to a switch. We're using Switch E for our flap channel. Now, set the switch in the middle position. This will be your 1/2-flaps setting. Adjust the flap linkage from the servo to the flap so that the flaps are at their 1/2-flaps position. In the "CH5 and CH6 Set" function, you'll adjust the full flaps position and the flaps up position. Enter the function and set the switch to your "flaps up" position. Adjust the appropriate endpoint so that the flaps are properly set in the "flaps up" position. Move the switch to the "full flaps" position and adjust the other endpoint to get the desired full flaps setting.
You're done.