A method includes accepting inputs to a marine vessel's control module, the inputs defining first and second waypoints and a desired heading, and defining a desired track between the first and second waypoints. Ideal steering and thrust commands required to orient the vessel at the desired heading and to maneuver the vessel from the first to the second waypoint are generated and carried out. The method includes measuring a current position and heading of the vessel; calculating a cross-track error based on the current position as compared to the desired track; and calculating a heading error based on the current heading as compared to the desired heading. The method includes generating corrective steering and thrust commands that are required to minimize the cross-track error and the heading error. The propulsion system propels the marine vessel according to the corrective steering and thrust commands, as appropriate.