The game commanders sold in the US are set to mode 2, but you can easily convert it between mode 1 and mode 2 by making some mechanical adjustments inside the controller. If you need the instructions, let me know.

If you fly your airplane in the same mode as helis, then your game controller is already in the correct mode as you have already set it up for airplanes without problems. The heli control functions in the basic or advanced setup menu are as follows:

For throttle/collective pitch, use the throttle/collective pitch function
For fore/aft cyclic, use the elevator/cyclic pitch function
For left/right cyclic, use the aileron/roll function
For tail rotor, use the rudder/tailrotor function

Just assign the controller channels to the functions, calibrate and you're set to go. You can create many configurations with your controller and save them under different names. For instance you could have one config for planes and another for helis, or you could use the same config for both.