There are a couple of National Archives publications that address records of the Southern Superintendency as follows:
- "Preliminary Inventories of Records of the BIA." 2 Volumes. Edward E. Hill, 1965.
- "Guide to Records in the NA Relating to American Indians." Edward E. Hill, 1981.
The Microfilm Collections in the NA are listed in "American Indians - A Select Catalog of NA Microfilm Publicans" 1984.
All these books should be available through ILL if not at your local library.
I believe LDS has most of the NA microfilm and for sure has microfilm of "Letters" and "records" of the Southern Superintendency for the period for which you are interested. Suggest you check out their catalog at www.familyserach.org
and enter "Southern Superintendency" in the key word search.