What do you mean by "doing the roof"? If you are going to put a special coating on the whole roof or replace it, don't install new vents until after the new coating or roof material.
If you use Eternabond, you wouldn't want to put anything on top of it. If you wish, you can put a small bead of Dicor lap sealant around the edges of the Eternabond. I put in a MaxxAir fan last summer, and used Eternabond for the first time. I really liked working with it and plan to use it when I replace the bathroom vent this year. And, I also plan to use it on the roof seams in the near future. It's easier to periodically inspect the Eternabond to make sure it's sealed properly than worrying about cracked sealant and dealing with Dicor.