In the National Archives is a collection that is listed in the Nationl Archives Preliminary Inventory 101 of the War Dept Collection of Confederate Records as "Miscellaneous Records of the Government of the Confederate States of America." I have a 1957 edition of the Preliminary Inventory and the description of these Miscellaneous Records begins on p 253 and runs through p. 268. I believe the "Manuscripts" you are looking for are described on p. 264: "A miscellaneous collection of manuscripts, mainly Confederate but including some Union...[that] includes correspondence concerning prisoners, deserters....." The manuscripts are numbered 1-7117. They have republished the Preliminary Inventory so these page references might not be exact, but should get you in the ball park.