Near the end of June, 1861, Hotchkiss signed on as a Confederate teamster to take supplies to the Churchville Cavalry at Rich Mountain, West Virginia. Hotchkiss offered his services as a mapmaker to Brig. Gen. Richard B. Garnett, whose Confederate brigade was operating in western Virginia. Hotchkiss served at Rich Mountain and created maps for General Robert E. Lee's planned campaign in the mountains. He took a brief medical leave after being stricken with typhoid fever, but returned to duty in March 1862 as chief topographical engineer of the Valley District, reporting to Maj. Gen. Stonewall Jackson. Following initial defeat the Battle of Kernstown during his 1862 Valley Campaign, on March 26, 1862, Jackson summoned Hotchkiss to his headquarters at Narrow Passage near Woodstock and directed him to "make me a map of the Valley, from Harper's Ferry to Lexington, showing all the points of offence and defence [sic] in those places." Hotchkiss' immediate recommendation was that Jackson's line on Stony Creek at Woodstock was indefensible, and that Jackson should withdraw to Rude's Hill, a defensible small promontory south of Mt. Jackson. It was at Rude's Hill that Jackson reorganized his command for the rest of his successful 1862 campaign on the Shenandoah Valley.