A method is provided for controlling a powered system including an engine operating on a plurality of fuel types. The method includes generating operational input signals from operational input devices, and generating a respective configuration signal indicative of a particular location of the powered system along a predetermined course comprising a mission. Additionally, based on the operational input signals, the configuration signal, and a respective engine emission profile for each of said configuration signal, the method includes generating control signals to a plurality of end use devices of the powered system to limit one or more of the total engine emissions of the fuel types, the total fuel efficiency of the fuel types, the total output power of the engine, a time of arrival of the powered system along the predetermined course, and/or a combination thereof.