A method and system(s) are disclosed for integrating a new fuel into an operating transportation system in a continuous, seamless manner, such as diesel fuel being gradually replaced by compressed natural gas (“CNG”) in long haul trucks. Integration can be implemented using two enabling technologies. The first is an engine system capable of operating seamlessly on two or more fuels without regard to the ignition characteristics of the fuels. The second is a communications and computing system for implementing a fueling strategy that optimizes fuel consumption, guides the selection of fuel based upon location, cost and emissions and allows the transition from one fuel to another to appear substantially seamless to the truck driver.