Within the last few weeks I saw an article in one of the Civil War "pulp" magazines on the rack at Barnes and Noble about Federal Indian troops ("regular" volunteer troops) at the Battle of the Crater, Petersburg (should have bought the magazine). A book-length treatment of Indians fighting on both sides is: Laurence M. Hauptman (1995) "Between Two Fires; American Indians in the Civil War." New York: the Free Press. Can't recommend it too highly, but it's a place to start.
John