After capture, the "Planter" required some repairs, which were performed locally, and went into Union service near Fort Pulaski. The boat was valued for its shallow draft, compared to other boats in the fleet. Smalls was made pilot of the under Captain Alexander Rhind. In June of that year, Smalls was piloting the "Crusader" on Edisto in Wadmalaw Sound when the "Planter" returned to service, and an infantry regiment engaged in the Battle of Simmon's Bluff at the head of the Edisto River. He continued to pilot the "Crusader" and the "Planter". As a slave, he had assisted in laying mines (then called "torpedoes") along the coast and river. Now, as a pilot, he helped find and remove them and serviced the blockade between Charleston and Beaufort. He was also present when the "Planter" was fired upon at several fights at Adam's Run on the Dawho River and at battles at Rockville, at John's Island, and at the Second Battle of Pocotaligo.