FMS 2.0 Beta 7:
Start FMS. Click on Controls (‘alt‘ + C), select ‘Analog control..’. Then select 'Joystick Interface'.
To set up the controls press Mapping/Calibration. Connect your transmitter. Press 'Calibrate' and follow the instructions. Then set up the Mapping. Move your rudder stick to see what channel it is on and enter the number in the channel box. Continue through the elevator, ailerons, throttle. The next 4 are the controls for the helicopters. I set these up in the same order as the first 4. The requirement for Inv (inverse) is best found by trial and error. Press 'OK' and you should be flying.