Norman, others will know more than I about this subject, but the answer is that some partisan units were at leat nominally under Army control, while other, usually smaller units operated independently, sometimes to the detriment of their best interests.

Probably the best known of the formwr type was John Singleton Mosby. A lawyer, he enlisted as a private, ended up in Stuart's cavalry, and was made an officer after being a successful scout and spy.

He was commissioned to raise a regiment in Northeastern Virginia, which became known as "Mosby's Confederacy". His men, when not engaged, stayed near or at their homes, until needed for a raid or mission assigned by the army. They harrassed the Union units in their area. When Custer allowed some of Mosby's men to be hanged as traitors, Mosby captured an equal number of Union soldiers, and drew lots to select the ones to be executed. The rebels' hearts were not in it, and some were not hanged, but shot, and not all were killed. Later, cooler heads prevailed on both sides, and there were no more reprisals.

The smaller, independent units, particularly in the west, were less bound by such niceties as the rules of warfare. This was true of both sides, especially in Missouri and Kansas, and in the mountains of the Carolinas, Tennessee, and Georgia. Animosities became very personal in some of those areas. Some folks who post on this board had family involved in some of these actions, especially as victims.

I have posted before about General Wofford taking charge in North Georgia in January, 1865, and establishing some degree of discipline over about 7000 men operating in the area, and of his surrender at Kingstom may 25, 1855.

There are a number of books listed on the board, or reviewed on the books board, which will fill you in. The Missouri board still has knock down drag out disagreements about the actions of Quantrill, Bloody Bill Anderson and others in that area. Sally probably has a handle on that issue. Good hunting. Stan