One faction of the Cherokees fought for the confederacy under Stand Watie, who was himself a slave owner. The other faction (in a split that went back to the Trail of Tears era, when Watie essentially sold out the others), were aligned with the Union. Over the course of the war, Watie's force was plagued with desertions as his men went over to the United States side.
Apart from Watie's troops (a few thousand at their peak), I don't think you can find another Indian group of any significance aligned with the Confederacy.
Most Indians fought with the Confederacy. Ragtail bands of Northeast Indians fought with the Union. MOST INDIANS sided with the Confederacy. Try reading some of my post and you might learn something. If any people on earth had a reason to despise the Federal government it was the American Indian. And after the war the murdering of Indians continued, with Sheridan and Sherman slaughtering them wholesale.