I always do mine side be side if I can fit them on the top rack. One less thing to deal with (cleaning the grate, taking the top grate off to deal with the bottom butt . . .). However, if they are far different in size, it is better to put the larger one on the lower rack IMHO. Since I don't use water, I think my lower rack is hotter which makes the cooking time between the two butts closer.