A marine propulsion control system for use with a marine vessel, includes a port side engine in electronic communication with a port side engine controller and a starboard side engine in electronic communication with a starboard side engine controller. A control station includes a port lever configured to control a throttle of the port side engine, a starboard lever configured to control a throttle of the starboard side engine, and a user interface. A propulsion control processor is in electronic communication with the port side engine controller, the starboard side engine controller, and control station. In a synchronized operating mode, the propulsion control processor transmits a throttle instruction to the port side engine controller and the starboard side engine controller pursuant to a throttle position of a master lever corresponding to the first of the port lever and starboard lever to be actuated upon activation of the synchronized operating mode.