There are “vast resources available to the researcher” at the National Archives.
This publication is suggested as a starting guide:
The Confederacy, A Guide to the Archives of the Government of the Confederate States of America, Henry Putney Beers, National Archives and Records Administration, Washington, D. C., 1986 536 pages
This “ . . . Guide describes all the records of the Confederacy at the National Archives, the Library of Congress, and in other custody.”