First, go into the Function section of the Linkage Menu and change Flap2 to Flap. Set the first Flap channel to the desired control. You'll now have 2 channels named "FLAP" that operate off of the same switch.

Move the switch to the "Takeoff" (mid flaps) position. Adjust the control linkages so that the flaps are in their proper positions. Now, move the switch to the "Flaps UP" position. Adjust the Travel endpoint so that the flaps are in the proper position when they are stowed. Finally, move the switch to the "Landing" position. Adjust the opposite Travel Endpoint so that the flaps are in the desired position.

Repeat this procedure for the second flap channel.

You will likely have to work with this a bit to get everything fine tuned. If you need to adjust the Takeoff flap position, you will wind up having to adjust both UP and Full down endpoints, but you will have the flaps operating as you desire.