For those interested in Watie, there are several books:
Cunningham, Frank. "General Stand Watie's Confederate Indians."
Sullivan, Roy. "Scattered Graves: The Civil War Campaigns of Confederate Brigadier General and Confederate Indian Chief Stand Watie."
Knight, Wilfred. "Red Fox: Stand Watie and the Confederate Indian Nations during the Civil War Years in Indian Territory." [Reissued by two other publishers with different subtitles]
Franks, Kenny. "Stand Watie and the Agony of the Cherokee Nation."
Bartels, Carolyn. "Stand Watie and the First Cherokee Regiment, 1861-1865."
Schmid, Vernon. "Watie's Wolves: A Novel of the Civil War in Indian Territory."
For the North Carolina branch of the Cherokee and the hard luck regiment that was raised to fight for the Confederacy, see:
Gaines, W. Craig. "The Confederate Cherokees: John Drew's Regiment of Mounted Rifles, 1861-1865."
and
Crow, Vernon H. "Storm in the Mountains: Thomas' Confederate Legion of Cherokee Indians and Mountaineers."
Godbold, E. Stanley. "Confederate Colonel and Cherokee Chief: The Life of William Holland Thomas."
Osprey has released 2 books:
"The American Civil War in Indian Territory" by John Spencer
and
"Native American Mounted Rifleman, 1861-1865" by Mark Lardas
For those who hate staring at a computer screen, the trilogy by Abel on Confederate Indians is also available in paperback.