Both of Robert Utley's books dealing with the Frontier Army provide good starting points. I'd also suggest focusing on the period from about 1866 to 1873 or so...that covers the immediate postwar period and the debate about who should actually administer Indian policy. Starting in 1874 you had the demise of Grant's Peace Policy and what might be considered a transition to more conventional warfare (both the Red River War and the Great Sioux War took place after 1873). While the Apache remained a threat until much later in the period, you have to navigate a whole flood of George Crook propaganda and there are significant gaps in coverage (mainly the period from 1860 until 1871 or so when Crook came on scene).

Ganluv is also correct in saying that it's difficult to lump all these conflicts into a single "war." There were simply too many differences.

I suppose you could consider the situation in Indian Territory and Texas to resemble population control, especially when it came to the Kiowa and the feeling among Army leaders that the reservations near Fort Sill did nothing more than provide safe havens for raiders hitting into Texas (which had no reservations) and then falling back to the Government "safe zone" provided by the reservations. That also ties into control of Indian policy...many within the Army always felt that they were better-suited to manage Indian policy and resented Grant giving that authority to the Indian Bureau and the Quakers (who provided a number of Indian agents and were usually hostile to the Army).

I could go on at some length about this stuff... But Utley's books are a good starting point and then you can drill down into specific areas and conflicts.