the GUI does two things...
1. IF you change any options from their defaults, the GUI copies the xml file to the $FGHOME/Input/Joysticks directory and applies the changes.
2. the GUI allows you to assign specific actions to the available buttons and axises that are recognized.
if you need something that is not an action or option available in the GUI, then you have to manually edit the file in $FGHOME/Input/Joysticks to add that action or option... an example of this might be to apply a certain amount of acceleration so the further you move the stick, the sharper the movement is instead of it being linear... another option would be to reduce the sensitivity of the stick so you have to move it further...
if you need something that is not an action or option available in the GUI and the necessary joystick file does not exist in $FGHOME/Input/Joysticks, then you need to manually copy the necessary file from $FGDATA/Input/Joysticks to $FGHOME/Input/Joysticks so you can edit it...
does that help?