Of significance, of course, is that Drew's Regiment, 1st Cherokee Mtd Rifles (Confederate) defected in 1862 and served the remainder of the war in the 2nd and 3rd Indian Home Guard (Union). The members of this regiment never intended to fight "the whiteman's war" but instead to protect the Cherokee Nation from invasion which initially was by Kansas jayhawkers raiding Cherokee settlements and stealing livestock.
There are a very few good books on the subject of the Indians of the Indian Territory in the Civil War. Regarding Drew's Regiment, I recommend Confederate Cherokees by Gaines. I always recommend Annie Abel's well researched The American Indian as Participant in the Civil War. The Prairie was on Fire by Whit Edwards is one of my favorites since it is based entirely on first-hand accounts of the war in the Indian Territory. Regarding the Union Indians there are Wiley Britton's first-hand accounts in Union Indian Brigade (the three Indian Home Guard regiments) and The Civil War on the Border.
Knight's Red Fox is about Stand Watie's Cherokee and is okay though rather over-glorifies their activities. There are several other books on Watie and his Cherokee regiments that are poorly researched and contain significant errors. Too often people believe that if it got published in a book, it must be true. That's like saying "a politician said it so you know it's true".
On another note, Cooper served to the end of the war in the Indian Territory and remained with the Choctaw after the war.
I would encourage you to post regarding the Indian Territory and Indian units on the Indian Territory message board instead of the Texas message board.
http://history-sites.com/itcwmb
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