The majority of guerrilla operations in Missouri were planned and conducted independently of Confederate regulars. However, some irregulars served as screen or security for behind-Union-lines Confederate recruiting and the movement of such recruiting bands starting in 1862. Their efforts were key to a number of southern recruiting command returning to their own lines with hundreds of needed recruits.
Beginning in autumn 1863 Confederate irregulars evidently directed by Confederate command conducted a vigorous sabotage campaign against Union river transport in several river ports in central United States including St. Louis. They were responsible for the destruction of a number of river steamers then in Union use.
Preparatory to Confederate General Sterling Price's autumn 1864 raid into Missouri, some Confederate officers traveled to Missouri from Arkansas and coordinated with a variety of the active guerrilla bands, especially in some of the counties lining the Missouri River. I am not sure of the details of this coordination, but when these guerrilla chiefs later met with General Price in early October he directed them to attack Union transporation facilites--especially railroads. Some of the guerrilla bands did attack railroad facilities in Missouri as directed, but their efforts failed to significantly deny the Union military use of those vital arteries.