Didn't Lee command the Virginia Militia force that tried unsuccessfully to keep Lincoln from prying loose West Virginia?
Lee was given command of Virginia forces (pretty much existed only on paper at that time; just a few militia companies) by the governer (Lechter, I think his name was). Almost immediately afterward he became Jefferson Davis’ personal military advisor, and remained in that role until he was given command of the ANV on June 1, 1862, after Johnston had been wounded.