Upton Hays organized what became the 12th Missouri Cavalry Regiment in the late summer of 1862. He was killed shortly after the regiment was organized and was succeeded in command by Colonel Beal G. Jeans. Jeans subsequently resigned his commission in August, 1863,David Shanks became commander of the 12th Missouri Cavalry. When Price began his raid into Missouri in the fall of 1864, General Jo Shelby was given a division, and Shanks assumed command of the old Iron Brigade. When Shanks was elevated to brigade command, William Irvin took command of Shanks' regiment. Insofar as I can tell, Shanks never served in the 6th, later the 11th Missouri Cavalry Regiment. That was called the "Southwest Cavalry", which was organized in the southwest part of the state. The 12th regiment, as you say, was recruited primarily in Jackson County.
This regiment (Hays'; Jeans'; Shanks) was usually referred to as the 2nd Cavalry in the Trans-Mississippi Dept up to the end of the war. But the Confederate War Department designated it as the 12th early on.
Hope this helps some.