Jamie --

I realize this is an old post, but you may wish to pick up a copy of Henry Putney Beers, The Confederacy: A Guide to the Archives of the Confederate States of America.

NARA sells a reprint for $25.00 plus shipping.

http://www.archives.gov/genealogy/military/civil-war/

If you ever have another question about whether this kind of document or another survived, this book will answer it.