Short answers, pulled from the story.
Colonel John B. Magruder was assigned to command operations on the lower Virginia Peninsula in May 1861, with Yorktown as headquarters. By the end of 1861 he had been promoted to major general and still led the force, which had grown to 13,000 men.
Confederate Secretary of War LeRoy Pope Walker ordered the Department of the Peninsula into existence on the 26th of May 1861. The military force took its name from the department.
The Army of the Peninsula fought at Big Bethel, an early Confederate victory in which Magruder used a portion of his command to good effect.
In April 1862 the Army of the Peninsula was incorporated into the right wing of Joseph E. Johnston's larger army as it prepared defenses against George B. McClellan. The army designation ceased to exist at that point.
By the end of 1861 the Army of the Peninsula had grown to 13,000 men, all still under Magruder's command.
Though absorbed into Johnston's force before the Peninsula Campaign began in earnest, the army's independence and initiative were instrumental in preventing McClellan from rapidly advancing on Richmond.