Helmsman with multiple joysticks/peripherals

Ahoy there! I recently started playing Artemis SBS, and am loving it. So far I have played as Weapons, Science, and Engineering in online play. I'd like to try Helmsman, but am having difficulty. I also play a combat flight sim called Rise of Flight, where I fly twin-engine heavy bombers. My PC is set up as a very nice sim-pit, with joystick, rudder pedals, throttle quadrant, TrackIR head-tracking, etc. This is great for flight sims, since I can easily adjust the numerous controls necessary to keep a huge twin-engine biplane bomber in the air. However, when I try to play as the Helmsman in Artemis, the game seems to be picking up some different control axes than what I'd like. How do I tell the game to read the X/Y inputs from my joystick, rather than the left and right toe-brakes on my rudder pedals?

Also, how do I check and configure the hotkeys for the different positions? I had several people tell me tonight that U and I are the hotkeys for raising and lowering shields, but they did not work for me and almost got my crew killed during a BvB duel.

Thanks!
-EM3 Kotori87