In previous control systems for engines that fuelled with a conventional fuel and an alternative fuel, a conventional fuel controller controlled fuelling for both fuels. This required extensive modifications to both the conventional fuel controller and an alternative fuel controller. A control system for an engine comprises a first control unit programmed to generate a first pulse width to actuate a first fuel injector to introduce a first fuel; a second control unit programmed to generate a second pulse width to actuate a second fuel injector to introduce a second fuel; and a communication line between the first and second control units. The first control unit determines a total fuel energy amount to be introduced by the first and second fuel injectors. The second control unit determines a first fraction of the total fuel energy amount to be from the first fuel and a second fraction of the total fuel energy amount to be from the second fuel.