 Thereafter, Harris was assigned to the staff of General P. G. T. Beauregard.Harris planned Confederate defenses of Centreville, Virginia, Fort Pillow, Island Number Ten, Vicksburg, Mississippi and Charleston, South Carolina.He was promoted to captain of Confederate engineers on February 15, 1862, to major on October 3, 1862, to lieutenant colonel on May 5, 1863 and to colonel on October 8, 1863.