The most authoritative source would be "The War of the Rebellion: A Compilation of the Official Records of the Union and Confederate Armies." (70 volumes in 128 serials.) (Washington, D.C.: U.S. Government Printing Office, 1880-1901.)

There is also a "Supplement" published over the last decade in 80 volumes.

Whit Edward's book, "The Prairie was on Fire: Eyewitness Accounts of the Civil War in the Indian Territory" (Oklahoma City: Oklahoma Historical Society, 2001) lists 107 "hostile encounters" (not all of which involved Watie/Watie's men).

You might be able to find copies of three out-of-print books [1] by Wilfred Knight, "Red Fox: Stand Watie and the Confederate Indian Nations during the Civil War Years in Indian Territory" (Glendale, California: Arthur H. Clark Co., 1988.) AND [2] by Kenny A. Franks "Stand Watie and the Agony of the Cherokee Nation" (Memphis, Tennessee: Memphis State University Press, 1979.) AND [3] Mabel Washbourne Anderson - edited with new material by Budd Parrish, "Life of General Stand Watie, the only Indian Brigadier General of the Confederate Army and the Last to Surrender." (Harrah, Oklahoma: Brandy Station Bookshelf, 1995, facsimile reprint of 1915 volume by Mayes County Republican, with new maps.)

See also:

Frank Cunningham's "General Stand Watie's Confederate Indians." (Norman: University of Oklahoma Press, 1998; paperback reprint of work originally published by The Naylor Company, 1959.) may also be helpful.

John C. Waugh's "Sam Bell Maxey and the Confederate Indians". (Abilene, Texas: McMurray University – McWhiney Foundation Press [Civil War Campaigns and Commanders Series], 1998.)