With the flaps on their own channel, go into the 'AUX' channel menu and set the flap channel you're using so that it's activated by a 3-position switch. Toggle the switch to the middle position. Connect the servo to the receiver and turn everything on. The servo will center. Set the geometry of the flap pushrods so that the flaps are deflected to the 1/2-flaps amount you want. Once that's set, go into the End Point menu. Toggle the switch to the 'flap up' position and adjust the endpoint so that the flaps are in the proper 'flaps up' position. Now toggle the switch to the full, 'flaps down' position and adjust the endpoint so that the flaps have the amount of deflection you want.

No need for mixers or such. Just set to a toggle, set linkages to half-flaps with the toggle in the middle, and set the endpoints for flaps full down and fully-retracted.