| On edit. Wikipedia mentions departments but provides no examples.|
The C.S. Army was composed of independent armies and military departments that were constituted, renamed, and disbanded as needs arose, particularly in reaction to offensives launched by the Union.
On edit again. Found this, seems to identify many if not all of the departments.
Textual Records: Letters and telegrams sent, registers of letters received, issuances, and other records of the Army of the Potomac (Confederate), 1861-62; Army and Department of Northern Virginia, 1862-65; Army and Department of the Peninsula, 1861-62; Department of Richmond, 1864-65; Department of Henrico, 1862-63; Department of North Carolina, 1861-62; Department of North Carolina and Southern Virginia, 1862-65; Department of South Carolina, Georgia, and Florida, 1861-65; Department and District of Georgia, 1861-65; Army of Pensacola, 1861-62; Central Division of Kentucky, 1861-62; Central Army of Kentucky, 1861-62; Army of Kentucky, 1861-62; Army of the Kanawha, 1861; Departments of East Tennessee and Western Virginia, 1861-64; Army and Department of Tennessee, 1862-65; Department of Alabama and West Florida, 1861- 62; District of the Gulf, 1862-65; Department of Mississippi and East Louisiana, 1864-65; Department of Alabama, Mississippi, and East Louisiana, 1864-65; Army of Louisiana, 1861; Army of the Mississippi, 1862-65; Department of the West, 1862-63; Army of the West, 1861-62; Western Department, 1861-63; Military Division of the West, 1864-65; Department of Texas, 1861-62; and Trans- Mississippi Department, 1862-65. [Read More]
Some further information.
Might be worth trying to find a library copy of: Eicher, John H., & Eicher, David J., Civil War High Commands, Stanford University Press, 2001, ISBN 0-8047-3641-3.
With occasional, fatigued glances at life's rear-view mirror from the other side of time.