I am not sure that after his term as governor that he had a Militia connect. I believe that he retire to private life at his home in Pine Bluff.
However being a recent ex-Governor of Arkansas, I am sure that he recieved his commission direct from Governor Rector and his military commission in Little Rock. His commission seems to be based more on political connections rather than his military experience. The 9th Arkansas Infantry was one of the first regiments raised from the state after the Battle of 1st Manassas (Bull Run) for Confederate service in July 1861 and as you point out he was acting as enrolling officer for that unit then.
He became a Brigade commander under Major Gen Earl Van Dorn. But refused to go east with Van Dorn's army in April 1862. Van Dorn left Roane in command of Arkansas while he was gone but did not leave any organized troops, A general without an army. But he was loyal to Arkansas and her defence.