ANSWER
The Confederate Army had no Chief of Staff, because Jefferson Davis preferred keep the responsibility related to on himself, with disastrous outcome.
Only at the last stage of the war R.E. Lee was appointed to that charge but it was too late to remedy the mistake and influence the course of the military events.
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Joe Johnston, until he was wounded at Seven Pines, then Robert E. Lee for the rest of the war, ending with his surrender to Grant at Appomattox.
None of the Above :)
General Lee of virginia led the confederate army and General Grant led the union army
Joseph E. Johnston of Virginia was the highest ranking US military officer to resign his commission and take command of a Southern army. He led the Army of the Shenandoah to reinforce General P.T. Beauregard's forces at the First Battle of Bull Run on July 21, 1861, where the total Confederate forces numbered about 32,000 men.
Antietam/Sharpsburg (Maryland)
In the April 1861 the battle of Fort Sumter led to the Union's surrender of the fort to Confederate forces.