I believe that John Baker Thompson played a part in the formation of the 1st Arkansas Infantry and not the 2nd battalion. I believe that through politics James Fagan was able to secure command of the 1st Arkansas when it was formed.
William Naylor Bronaugh a Graduate of University of Virginia and entered service as a 1st Lieutenant of Company "D" Clan MacGregor, under the command of Captain Donaldson MacGregor of Fagan's/Colquitt's 1st Arkansas Infantry.
Lieutenant Bronaugh travel with that regiment in it's journey to Lunchburg, Va. where the Regiment was muster into Confederate Service. The 1st Arkansas was 2 companies short of the necessary regimental strenght of 10 companies. Lt. Bronaugh was sent back to Pine Bluff where in he recruited three comapnies from Jefferson, Saline and Hot Springs counties which were mustered into Service September 3rd, 1861. How he obtained this assignment exactly is unknown. But it is obvious that he had some support from powerful allies in the 1st Arkansas possibly Baker and MacGregor and possible in the higher command structure in Virginia. In any case he was one of the few Arkansas commanders who were thought highly of by the Virginia authorities in 1861 and early '62.
Anyway these Companies returned with Bronaugh to Virginia where they found the two other comapies had been consolidated with the 8 companies of Arkansasawyers and the 1st Arkansas was at full strenght. So these companies were attached to the 1st Arkansas as the 2nd Arkansas Battalion and Bronaugh because of his Virginia heritage and his University of Virginia connections was appointed as Major of this battalion.
Because of the difference of enlistment dates when the 1st Arkansas was transferred back west in January 1862, the 2nd Arkansas Battalion remained in Virginia to become history.