You have not mentioned the Confederate Partisan Rangers established in 1862? by the Confederate legislature. My understanding of the role of the Partisan Rangers was that they were to conduct actions against the Union forces, which included state militia, interdict supply and communications and were to be supplied by the Confederate Army. I don't know much about other Missouri areas, but in Jackson Co. the Confederate guerilla Quantrill became the leader of the Partisan Rangers in that area when Col. Upton Hays joined the Confederate Army with his 2nd Missouri Cavalry Regiment. Quantrill's commission as Captain was authorized by the Confederate leadership. It seems to me that the Confederates failed to estabish an unambiguous chain of command so that the guerilla companies understood generally their role in the war in regards to the Confederate war effort and cooperated with that effort when asked - if they could. Beng more or less on their own in Union occupied territory they made their own decisions as to their actions based on local situations and their limited understanding of Confederate policy and goals.