If you haven't booked Black Hills yet, you might check out Rafter J. We stayed there two years ago and my kids loved it. It's a large campground with all the kiddo amenities. A trip to Blackhills could also be complemented by a side trip to the Badlands National Park. Custer State Park was ok but the Wind Cave tour was really enjoyed by my kids. We also enjoyed a picnic at Sylvan Lake (backdrop from a scene from one of the National Treasure movies). You can catch that on the Needles Highway drive which was really cool.
As for Yellowstone, just remember it is a very big place. From Cody to the Grand loop is almost 80 miles and nearly 120 miles to Old Faithful. West Yellowstone is better situated, IMHO, to most of the things you may want to see. To make a grand generalization, the West side of Grand Loop Road is where you can catch most of the geothermal sites and the East/NorthEast would be great for wildlife. NW corner has Mammoth which is a primary spot, SW has Old Faithful, tons of places to stop and see mud pots, geysers and hot springs between the two, plus Firehole River where many people like to swim. The NE drive out the Lamar Valley is beautiful with the Bison, antelope etc. Chance to see Grizzlies or Black Bears and if your lucky the wolves will be out. To be fair though, the wildlife is all over but there is a reason the Lamar Valley has been called the Serengeti of North America. Continue further NE out of the park to drive the Beartooth highway which is rated one of the top drives in US. East side has the falls and the Grand Canyon which are a must see and don't be surprised if the Bison bring traffic to a stand still.
The Grand Loop is not a highway so plan your activiies that allow for slower speed two lane roads and some sloths... err I mean a RV or tour bus. There will be the occasional wildlife traffic jam which could be a Bison walking down the road or standing in the road and refusing to move, or just people stopping to see wildlife and there will be places where you may decide to just pull over and see something you hadn't planned. Park food is pricey and definitely not on Zagats ratings radar. We packed lunches and some dinners. Best dinners were sausages and hot dogs grilled on a small portable propane grill while hanging out by one of the many rivers. West Yellowstone has all the amenities you should need and it also has a wildlife preserve where you can see bears and wolves up close along with other wildlife. It was a big hit with my kids. Hope you have a great trip!