in one of the older novels, I want to say it was in the warrior series, a pilot who normally ran a warhammer was commenting about how his left arm had nothing to do while running a panther because all the weapons were run from the right arm "stick"
the impression I always had based on that was that for something like the warhammer, there were essentially 2 hotas joysticks one attached to the right and left side of the pilots seat, that you controlled the weapons with. so you would have 2 main aiming reticules (mostly for the ppc's in the warhammers case) and then you would have various triggers, such as a finger trigger (typically for the ppc) and additional triggers like thumb triggers, such as you get on a good joystick that would be used for additional weapons, although it would be reasonable for the specific triggers to be assignable, but you might have 4 or more separate triggers for different weapons.