Based on your list, you will be heading north on 25 from Denver. So from Colter Bay as a base you will want to visit Jackson Hole, and do a day trip to Old faithful (about 2 hour drive one way with in season traffic) since you will be closet to the east entrance. I would also suggest a float trip down the Snake, great fishing or just sight seeing at the base of the Tetons. Use this link, http://www.trianglex.com/jackson-hole-river-trips
if anyone in the family likes horse riding this is also the best place to get a horse or join one of their trips into Yellowstone for a day, you will see wildlife and views on the horse trail that you will never find another way during tourist season in Yellowstone. The family that owns the Triangle X are great and will bend over backwards for you.
Then from Bozman you can drop back into Yellowstone at the North entrance to see the Hot Springs .