Most gimbals have servo inputs so the gimbal stays level, but if you change the inputs you can change the angle the gimbal is at.
Are you trying to use the GCS to fly the copter?
GCS Options -> Controller shows setup for an 8 axis joystick (at least it does under Linux), but it only allows mapping the joystick axes to the normal flight functions, so I think it would require code changes.
Does your head tracker insert signals in the PPM stream or what?
I would advise skipping the GCS joystick. If you want to use a computer joystick, there are plenty of projects that will give you a PPM stream from a joystick. Google:
joystick PPM
Most RC transmitter output PPM from their trainer ports too, so you have a joystick and PPM converter all in one box with that.
Add to the PPM stream with the head tracker, feed the resultant PPM stream into an OpLink. Using say a Revo in the copter, you could configure the head tracker signals to come out of the two unused servo-ESC outputs and connect those to the gimbal inputs.
It would probably be easier to just use a normal RC transmitter/receiver and something like this (first one I ran across):
https://hobbyking.com/en_us/quanum-3-axis-no-drift-head-tracker.html