They didn't have a General-in-Chief until the last few weeks of the war, and then it was the only possible choice: Robert E. Lee.
Before that, the Confederate President, Jefferson Davis, saw himself as a virtual General-in-Chief, but he was hopelessly out of his depth, both in military and civil matters.
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There was no General-in-Chief until January 1865, too late to make any difference.
Up till then, the Confederate President Jefferson Davis had tried to double in that role.
When the post was eventually created, it was given to the only possible choice, Robert E. Lee.
Confederate army was the name. They were also called Rebels too.
the confederate states army
Robert E. Lee
During the course of the war, one million men fought for the South
Robert E. Lee was the general of the Confederate Army for the vast majority of the Civil War.