As far as I know m8, there's no problem with having more than 1 stick installed in Windows. You just need to ensure that the axes in-game are mapped to the correct controller. As I'm also going to be using the throttle component of my X52, I intend to map the throttle slider on the MSFFB to a separate control (probably pitch trim) after all, the computer and game have no awareness that this input is 'supposed' to be the throttle, so you could map it to whatever you like.
My current thinking having done a little research is to use a BU0836A joystick controller board and run the following on an external panel.
Magnetos x8 - (Thinking ahead to 4 engines!) - Throw Switches
Fuel Cocks x4 - (Ditto) - 3 posn Rotary Switches
Nav, Landing and Cockpit lights plus Gunsight Illumination - Switches
Pitch, Roll and Yaw Trim on sliders (Free single rtation pots)
First step will probably be a proof of concept just for the lighting (I know, I'm a coward - lol)
Jabo