There is very little on the role of the Seminole during the war. There are a few articles in the Chronicles of Oklahoma related to the topic.

http://digital.library.okstate.edu/Chronicles/v012/v012p055.html

http://digital.library.okstate.edu/Chronicles/v033/v033p512.pdf

The best overall history of the tribes of Indian Territory during the war are in Annie Abel's three volumes: The American Indian as Slaveholder and Sessionist, The American Indian in the Civil War, and The American Indian and the End of the Confederacy. Some info on the Seminole is of course contained in these books though unfortunately there is not much. Abel's main sources are the papers of the Indian Office (the predecessor to the Bureau of Indian Affairs) and the Official Records of the War of the Rebellion. I believe the full text of all three are online in Google Books.

The best military history of the Indian Territory in the Civil War, in my opinion, is "The Prairie was on Fire" by Whit Edwards. Though again it is not specific to the Seminole and, due to their relatively small size and limited role, it doesn't contain much about them. It is highly accurate though and relies heavily on first-person accounts.

I hope others will respond with sources I'm not aware of.

Ken