Unfortunately if you are using your own controller, you have to set up a CONTROLLER configuration for each plane in the sim.

In the edit screen you can assign which channel ( stick, switch or knob on the TX ) controls what device, surface, etc. on the plane.

If you expand the entries on the CONTROLLER edit screen, you can move the sticks on your TX to see which axis, switch, etc. the sim sees when you move something on the TX... then you can assign the respective ones to the virtual plane.

It's a hassle because you have to do this for each plane or heli.

The FSOne controller is much easier, but it's centering and registration is just awful.