You might try looking in the records of the Confederate Secretary of War in the National Archives, especially letters sent and received. Here is a summary of those papers in Record Group 109 of the Confederate Records from the National Archives Web Site.

109.6 RECORDS OF THE OFFICE OF THE SECRETARY OF WAR
1861-65

Textual Records: Letters and telegrams sent, 1861-65. Letters and telegrams received, 1861-65, with index. Records relating to personnel and accounts, including War Department payrolls and requests for funds, 1861-65. Arrest registers and other records of the Richmond office of the Provost Marshal, 1862-64. Records relating to passports, including records of the passport office at Richmond, 1861-65, and records of passports issued at various locations, 1862-64. Letters sent, 1862-65, and other records of the Agent for the Exchange of Prisoners, including muster rolls of paroled and exchanged Confederates, 1863-65, and letters and reports on the Confederate prison at Andersonville, GA, 1864-65. Miscellaneous records, 1861-65, including record book of persons taking the Confederate oath of allegiance, n.d., and copies of military and naval laws and regulations, 1861-64.

Microfilm Publications: M409, M437, M522, M523, M524, M618, M901.