Read Battey's History of Rome and Floyd County. He is presented as a stalwart Confederate who protected the people from hogback Unionists. Same attitude displayed by several writers in Cherokee County, AL. Gatewood took the cattle and horses he stole at Chattanooga and distributed them in Cherokee (and the people of the area protected him, even ambushing a Union army column). A post-war writer in Pickens County hinted that he could call on Gatewood when the Unionist loyalists got too bad. Walker, Chattooga, and Polk (TN) Counties certainly despised him.
Did he do his raiding under Confederate authority? I have seen nothing to indicate he was anything but a guerilla. His sympathies seem to be pro-Southern but he deserted from the Confederate Cavalry in 1863. You're right that several units were sent (near the end of the war) to protect certain areas. Tom Polk Edmondson, and Co. F (I think) were sent to protect Murray/ Whitfield County (and keep and eye on Union activities at Dalton) by Wheeler. I don't think Gatewood was such a man.
There were a bunch of tiny outlaw bands all over NW GA who made life miserable for those unprotected by one of the armies. One of the groups in Polk County, GA was made up of a company that had been captured and paroled at Vicksburg. He claimed he was trying to raise a company for CSA service, but all he was raising was cane.
This subject is fraught with difficulties because so much of what Gatewood (for example) did could be interpreted two different ways. Did Gatewood kill a Union band in Chattooga County because they were cutting into his pillaging activities or because they were disrupting Confederate citizens? Who knows. Probably a little of both.
More later. Zack