Should work. Just make sure theyre both nvidia cards or amd card, otherwise you'll run into a world of hurt with drivers clashing together. Even then, im not sure if quadro series has its own drivers that might conflict with regular nvidia drivers. You'll just have to switch you monitor cable whenever you want to switch cards
^ This may resolve your issue (if you run Win XP). It was originally intended for laptops, but found many uses for desktops as well.
However, Windows Vista/7 did away with this feature.
Correct me if I'm wrong, but I thought that the Nvidia Control Panel allowed you to choose which GPU to run whichever application. I did this with my previous laptop. I was able to choose between the Intel on-board or the Nvidia Quadro 4200M for a specific application, or globally. This way you could point your office/work applications to the Quadro GPU, and the gaming apps to the "gaming" GPU.
^ I have similar on my laptop (can choose between intel igp or nvidia discrete), but I thought those were always special drivers. At least for me, I can't use regular nvidia drivers that they release.
Also op, its very easy to install 2 different o/s on 2 different drives. Usually the last one you install (win 7 for example) will allow you to pick which o/s you want to boot from when you start your computer. Either that or just push f8 and choose which hdd you want to boot from.