Knowles's commission was confirmed on 28 May 1776 and he was appointed as second lieutenant of the 28-gun , then under the command of Captain Charles Thompson. He served aboard the "Boreas" at Port Royal, and later on the North American Station at New York after the Battle of Bunker Hill. He was promoted to first lieutenant and in 1776 moved aboard the 50-gun , which was at that time the flagship of Vice-Admiral Molyneux Shuldham. He went on to see service on the flat boats at New York and Rhode Island. Knowles returned to Britain aboard in January 1777 to see his father, who was in declining health. Whilst at home he took the opportunity to prepare his first signal book, "A Set of Signals for a Fleet on a Plan Entirely New", for publication, before returning to the Americas in summer 1777. The book, published that year, proposed innovative new ways of flying numbered signals, and the development of tactics whereby the traditional line of battle would be abandoned once the battle began. It has a real Nelsonic ring about it. “..the book as a whole seems an astonishing achievement for a young man of twenty-four - even with Nelson’s captaincy at the age of twenty in mind…..all mark Knowles as a true innovator". Knowles claimed to have communicated the work to Lord Howe, and that Howe's tactics at the Glorious First of June reflected Knowles's theories on effective naval tactics. The death of his father on 9 December that year and his succession as the second baronet caused Knowles to return to England again.