It's mostly in the sauce, but the meat as well. SC style is focused on just certain parts of the pork shoulder, mainly the boston butt, and uses a mustard based sauce that isnt bad but not my favorite. Go to maurice's in columbia for the benchmark SC mustard sauce, it's the most popular (albeit a little controversial). The NC style utilizes the whole shoulder or even goes whole hog, and the sauce usually has more vinegar in it. Further, NC is split up into east and west, with west focusing more on just the shoulder and has a sweet ketchup based sauce that often has brown sugar or molasses in it, and east is whole hog with a thin vinegary peppery spicy sauce.
My personal favorite sort of combines several aspects of all of it, I smoke boston butts or shoulder roasts mostly, and my favorite is the eastern NC pepper vinegar sauce. The tang of the vinegar goes really well with the pork, but it doesnt mask the flavor of the meat and smoke. Good BBQ shouldn't need any sauce at all, and the sauce is just there to accentuate it.