Jason, if you have a lot of external fat, on a butt, that isn't rendered-down, you probably aren't trimming the raw butt enough. I buy my butts at Sam's, and they're generally pretty well-trimmed. But, they still need a little touch-up. Boston butts have enough internal fat that you don't need a thick fat cap to keep them moist, like a brisket. I trim almost all of the external fat, as well as the connective tissue between the two muscles (that flap on one side of the butt). I don't trim them naked, but definitely anything more than 1/4" or less. The result is no big unrendered fat chunks in the pulled meat. The internal fat will easily melt into the pulled meat, and isn't noticeable. Plus, without all the external fat, you get better brine penetration (if you brine), and better rub coverage on the meat for killer bark!
Just the way I do it, and it works for me!