You need to be a little bit careful. There was a difference between the Marine Department and the Marine Service. If he transferred to the Marine Department, he was working for a division of the Quartermaster Department. The term Marine Service could have meant he had been discharged to crew a blockade-runner. From time to time soldiers still on active service would be "loaned" or detailed to runners. Do you have anything that says "Confederate States Merchant Marine Service"? If so, he was not part of the Marine Department, or at least not on active duty.