I don't know much about the Commissary, but there is a relatively new book on the subject, Jerrold Northrop Moore's Confederate commissary general : Lucius Bellinger Northrop and the Subsistence Bureau of the Southern Army (Shippensburg, PA : White Mane Pub., c1996). It seems to be about the Commissary Gen'l, but it may shed some light on operations within the states.

As far as the subsistence officers in Alabama, Major John J. Walker was appointed 25 June 62 as chief of the subsistence department with Gen'l Bragg's Army of Tennessee. He continues as Commissary with AOT until at least 17 April 63 and appears to have taken over the office of Alabama State Commissary by 4 July 63. His appointment was dated 15 April 63. In it, it is explained that ...

"A chief purchasing commissary of this bureau will be selected for each State in the Confederacy, who will divide his State into districts (say some four or five, with a chief purchasing commissary or agent selected for each district, whose duties shall correspond in his district with the duties of the chief commissary in the State, these districts to be sub-divided, and sub-commissaries or agents selected for each sub-division), who will control and direct all purchases and business done by these district commissaries or agents, and, through them, their sub-agents. The chief district commissaries or agents will be nominated by the chief State commissary to this bureau for appointment, and their subagents or commissaries shall be nominated by the chief district commissaries or agents to the chief State commissary for appointment, upon the approval of this [CSA Subsistence] bureau."

One of Walker's nominations was Major W. W. Guy, apparently placed at Montgomery, date unknown. The only other personnel I found in a cursory check of the OR was Capt. V. M. Byrnes, an assistant to Major Walker.

As to fisheries themselves, this from Commissary Northrup:

"While recognizing the possibility that our fisheries would be destroyed by the enemy, it was still deemed advisable to establish them on our coasts and bays; accordingly, they were arranged in a number of places on the rivers of Virginia and North Carolina, on the Gulf coast, and at Mobile, and have afforded a supply of fish, both fresh and salt. As was anticipated, they have been frequently interrupted by the movements of the enemy, and many of them entirely broken up. Much was expected from those in Florida, if unmolested, and from them some results may yet accrue.
Respectfully, L. B. NORTHROP, Commissary. General C. S. Army." [dated 11 Feb 65] and

"By orders from the proper military department detail 10,000 men from the several armies, selected for their fitness for this service, such as disabled soldiers, new conscripts, and men over forty-five (if found necessary), who shall be placed under proper officers at the best fisheries to be found in the Confederacy." [Recommendations from the Commissioners of the Confederate States, Marietta, GA, 24 Oct 63] ... which might explain some of the men assigned to Mobile mentioned earlier.