Rupert S,
To check if the joystick is working correctly use the js_demo program.
It allows you to check the name of the device and the order of axes
and buttons and is described on the README.Joystick.html file.
This program should be inside the bin/ directory below the flight-gear
main directory and the architecture subdirectory.
After checking it works correctly, check the data/Input/Joysticks
directories of flight-gear.
You may find a definition file for your joystick in XML which you can
edit it to your liking.
Afterwards check the joystick.xml file on the data/ subdir of flight-gear.
You can force the default device to point to the file you edited/created.
If you need a definition file for a CH Fighterstick USB just say so, as
I have built one from one of the definitions already present.
I hope this helps
CS-DNA