If you look in...
ACW\GameData\Factions
You will find...
1Confederate.fac
0Union.fac
(amongst others) where you can create, edit, etc., all armies (add as many as you want in a theatre). Something that could be developed, and tested by modders, then possibly added by AGEOD (instead of them doing the grunt work). Something I am toying for as a part of my mod (adding a few extra per theatre).
Extra armies, from what I have found...
Army of the Kanawha (CSA in West Virginia)
Army of the Northwest (CSA in West Virginia)
Army of the Peninsula (CSA in Richmond Peninsula)
Army of Missouri (CSA in Missiouri)
Many other 'armies' out west consolidated into the Army of the Mississippi/Army of Tennessee (CSA Basically State Troop commands 'federalized')
(Central Army of Kentucky, Army of Middle Tennessee, Army of Louisiana, etc...)
Army of West Virginia (USA to replace W.Virginia Command)
Army of the Mississippi (USA to replace Mississippi Command)
Army of Georgia (Late USA army)
Army of the Shenandoah (Patterson's Command in 1861)
Army of the Gulf (Command based on New Orleals)
Also, this website is pretty extensive showing confederate departments and armies, along with their general history.
http://www.csawardept.com/history/armies/index.html