I would recommend Whit Edwards' "The Prairie was on Fire" which includes a chronology of minor and major engagements. It has a couple of minor errors but, unlike Ralph, I charge extra for "correct answers" ;-) All in all, this is my favorite book of the Civil War in Indian Territory. It is predominately based on first hand accounts.

As for just Watie's men, Wilfred Knight's "Red Fox" is pretty good. I would not recommend any of the other books on Watie.