Robert E. Lee was the best known of the general officers in the Confederate Army. Like many others, he was a former officer from the U.S. Army prior to the Civil War. Interestingly, Lee chose to wear the insignia of a Confederate colonel throughout the war. All the Confederacy's military forces answered to their President, Jefferson Davis, commander-in-chief of the Army, Navy and Marines of the Confederate States.
According to Wikipedia, on May 16, 1861, legislation was passed which stated: "That the five general officers provided by existing laws for the Confederate States shall have the rank and denomination of 'general' instead of 'brigadier-general', which shall be the highest military grade known to the Confederate States..."
In September, 1862 , when lieutenant generals were authorized, the Confederate Army had four grades of general officers: brigadier general, major general, lieutenant general and (full) general. These positions were nominated by the President and confirmed by the Senate.
By the war's end the Confederacy had at least 383 men who held the rank of Brigadier general, and 88 Major generals. There were 18 Lieutenant generals.
Originally, the five officers in the South appointed to the rank of General (Full general) were Samuel Cooper, Albert Sidney Johnston, Robert E. Lee, Joseph E. Johnston, and P. G. T. Beauregard, with their seniority in that order. Braxton Bragg was appointed a general when Albert Sidney Johnston died in combat, and Kirby Smith was appointed general to command the Trans-Mississippi Department.