We have stayed at the KOA in Custer, the Rafter J Bar in Hill City and Elkhorn in Spearfish. These cover the range from the south to the northern areas you're likely to want to see.
Custer State Park is beautiful and if you can get a site that suits you I'd do it, but realize you'll be on the southern end of a very interesting area. 3 weeks ago we were at Elkhorn, which is a beautiful campground north of everything.
I'd recommend looking at the Rafter J Bar, which is in the middle of everything. There's also a KOA near the Rater J Bar that others have liked.
