I was in your position just a couple weeks ago myself. I always run Nvidia but you know how that goes for mining so I wanted to put some ATI cards in my main system too.
Put in a 5970 and nope, let their specific drivers install (downloaded) and rebooted and nope, no problem at all. Afterburner or other temp tools might require a dummy plug or your monitor plugged into one or the other card to show all the temps sometimes but you can get it to work just fine.
If you're presumably going to be installing the ATI card in a slot below the first then shouldn't have any problems. For my cooling and how my fans are placed, I had to swap out my whole PCIe layout to make it work. Different case though. My main NV card is for example, in slot #7 atm.
Awesome, thanks for sharing your experience!
That sounds exactly like my situation.
My GTX480 will (hopefully) stay where it is, and I'll add 1x5790 or 2x6950 depending on what I can get at a reasonable price.
I plan to watercool all (2 or 3) cards, so space shouldn't be an issue.