Can I run 2 sepersate PCI-E cards

You should be able to. I'm running a 5850 and a 9800gtx. Whats your OS? I think it only works for windows 7 and xp, no vista.

Are you trying to run them separately for multiple monitors? Or are you trying to use one as a dedicated PhysX card? Because people have tried it out and found that if you already have any kind of decent nvidia card, and you try to add a second one for PhysX, all it does is generate more heat and sometimes slows the machine down too.

If you have two cards from the same manufacturer I dont think you need to install a second set of drivers for the second card as long as the first set of drivers is able to support both cards. Im about 75% sure on this.