Shawn, I was also part of the confused crowd when I first started reading about Arkansas Confederate regiments as a teenager. I, too, wondered how the "3rd Arkansas" could have gotten back to Arkansas after Sharpsburg to fight at Prairie Grove, and then gotten back to Virginia to fight at Fredericksburg. A little research revealed there was more than one regiment called the 3rd Arkansas.
That single question is what started me on my lifelong obsession with Arkansas regiments, their organization, and their designations.
And, Lord yes, Missouri designations are just about as froggy. Fortunately, we have a guardian angel in the person of Jim McGhee who has devoted years of research to sorting them out. Jim is in the process of publishing a guidebook on Missouri regiments. I can't wait. It's going to make my life much easier as I try to track down Arkansas soldiers who served in Missouri regiments.