If your going to anti-sieze them, just make sure you check them every 1000 miles or so for looseness.
My gasket kit came with new nuts that had a saraded flanges that bite into the retaining plate but you are spot on with the check them position, if nothing else the gaskets will tend to settle a little and if you don't tighten them, you could blow out a gasket in a short amount of time.
Thanks guys! I used a dab of anti-seize and everything went back together just fine and works well. I'll check them again in a few hundred miles and make sure they are still torqued properly.