Absolutely. The first regiment enrolled in Confederate service was the 1st Alabama Regiment, March 27, 1861. All units in service prior to that date had no higher authority than the state, because there was no higher authority until then.

For that matter, immediately after secession, the State of Mississippi should have a constitution as an independent state. Alabama does. Companies called into service by the governor under this constitution were called the Army of Alabama. As soon as Alabama joined the Confederacy, a new consitution was issued which acknowledged the the state as a member of Confederate government. Members of the Army of Alabama were turned over to Confederate service on May 11, 1861. They came from every corner of the state and formed the 1st Alabama Artillery Battalion, six companies, serving at Forts Gaines and Morgan until both surrendered during the summer of 1864.