I cook beans in my FEC at a temp of 250 for about three hours. I usually put chopped up smoked pork in mine so I don't really worry about cooking them under a butt. Plus, when I did cook it under a butt, I found they got a little too greasy.
Also, if you cook the beans too long, I find they get mushy. So I only cook them until they hit a temp of 170-180*.
One other thing I do that Dr. BBQ taught me is that I pour off some of the liquid from the can before putting in the rest of my ingredients.