If it is the blue bars in FMS that moves, you are almost there.
To calibrate/setup a joystick in FMS, start FMS.
- Go to Controls, Analog Control, Joystick Interface.
- Click on calibrate, and follow on-screen instructions.
- Move trottle on transmitter, and note which bar moves.
- Under mapping, enter the bar number that moved, next to Throttle.
- Repeat for ailerons, rudder & elevator.
- If the control works the wrong way, select Inv for that channel.
Hope this will help.