For Missouri Gray Ghosts of the Confederacy: Guerrilla Warfare in the West, 1861-1865 by Richard Brownlee, Inside War: The Guerrilla Conflict in Missouri During the American Civil by Michael Fellman and Monahan’s The Civil War on the Western Border will repay examination. For Middle Tennessee and Kentucky I don't have the books at my fingertips but will dig them out and get back. For Maryland, family history but there is an interesting note in Daniel Mogelever’s adulatory bio of one of the most problematic characters of the WBTS Lafayette Baker, ‘Death to Traitors’ where a raid through southern maryland in late 1861 by I think the 2nd Indiana Cavalry describes casually shooting unrepentant rebs (civilians) .
Plundering , thieving, abuse of non combatants was far to much the rule with yankees in the rural South.