You wouldn't be the first one to use more than one joystick at the same time. I have the stick part of my HotasX behind the screen. One fellow had a CH gameport throttle connected to a plastic food box containing the innards of the CH stick. You can even tear the stick apart and build an entirely different housing around the buttons and pots for a personalized controller.
Wow.. is there some way to save all your settings then
Radio shack use to have an assortment of project boxes for just such a mod. Not sure they still do but worth a google. You might even google the mod. Someone may have already done it like Bizman on the X