In the years leading up to the war, Watie was the leader of the mixed-race Cherokees, while John Ross, chief of the tribe, was the leader of the purebreds. This is quite ironic, though, since Watie was seven-eighths Cherokee while Ross was a Scotsman with only one-eighth Cherokee blood. The mixed-bloods, who had a long history of interaction with whites, had mostly favored the treaty by which the tribe was removed from the Southeast, while the full-blood Cherokees largely opposed it. The split led to a bitter feud between the two factions that resulted in the deaths of Watie's brother, uncle, and others and that continued clear up through the Civil War. There's a lot more to the story, but that's the very short version.
Stand Watie is buried at the Ridge cemetery just west of Southwest City, Missouri, a mile or so inside Oklahoma.