Good question. Usually this is no problem as the separate Saitek Throttle Quadrant you can buy has a USB connection, so you just plug that in, it detects as a new controller, and then you just make the assignments in FSX. But since you have a PS2 connected one, that could be more troublesome. I have never had any other customer ask this, and never tried it myself. My first thought is a PS2 > USB converter plug, but these are never guaranteed and often don't work all that well, but if you can find a converter cheap enough it may be worth a try. It looks like you can get these on ebay etc for a couple dollars. If that worked, then it would be straight forward. If not, I am not sure how else you would do that.
As for the knobs, they can simply be pulled off each lever stem and switched over no problem. As to how to program them, you just make the assignments in FSX. There are individual assignments available for Engine 1 throttle axis, Engine 2 throttle axis, Engine 1 prop axis, Engine 2 prop axis, Engine 1 mixture axis, Engine 2 mixture axis etc, and you just assign each lever to the desired axis. This is fairly easy.
The biggest problem is trying to correctly convert that PS2 signal to USB so you can attach it to your PC. If that can be done with 100% functionality of the quadrant, then the rest is easy.