There is provided a method for controlling engine valves of an internal combustion engine adapted to selectively operate at one of a first open position and a second open position, including controlling engine operation during a transition from a first to a second combustion mode. The method comprises determining a desired engine airflow based upon an operator torque request. A cylinder intake volume is determined for the desired engine airflow when operating at the first open position. A control scheme is determined to control the engine valves to attain the cylinder intake volume for the desired engine airflow when operating at the second open position. The control scheme is executed and the engine valve is transitioned to the second open position when the cylinder intake volume to operate at the second open position is within a range of authority of the engine valves.