JR,
Well i assume you are taking a butt and cooking it fat side down since you say the bottom. My recommendation is to leave the majority of it there and get rid of it after cooking. If you are cooking fat side down it can protect the meat from the heat. To me your post is vague since there are other questions I would like to ask... like are you cooking directly on the grate or are you cooking in a foil pan which depending on the fat content could create too much braising liquid in my opinion.
I like to take two boston butts and orient both money muscles in the same direction and deal with the fat removal and cutting/slicing/pulling after the cooking.
I used to trim, but now I just leave it. To me, it's easier to remove after it is softened up in the cook. I like short easy prep work. IMHO If your going to trim, get it close to the meat so you at least get good bark that you can eat.