The annual reports of the Commissioner of Indian Affairs make for good reading. Indian Territory was reported as part of the "Southern Superintendency." Here are direct links to the relevant reports (you will need to copy/paste into your browser):

1861: http://digicoll.library.wisc.edu/cgi-bin/History/History-idx?type=article&did=History.AnnRep61.i0005&id=History.AnnRep61&isize=M

1862: http://digicoll.library.wisc.edu/cgi-bin/History/History-idx?type=article&did=History.AnnRep62.i0008&id=History.AnnRep62&isize=M

1863: http://digicoll.library.wisc.edu/cgi-bin/History/History-idx?type=article&did=History.AnnRep63.i0010&id=History.AnnRep63&isize=M

1864: http://digicoll.library.wisc.edu/cgi-bin/History/History-idx?type=article&did=History.AnnRep64.i0015&id=History.AnnRep64&isize=M

1865: http://digicoll.library.wisc.edu/cgi-bin/History/History-idx?type=header&id=History.AnnRep65a

Here is the general link if you want to read up on other years as well: http://digicoll.library.wisc.edu/cgi-bin/History/History-idx?type=header&id=History.AnnRep65a

Enjoy!