A first control system for an engine includes first and second control modules. The first control module determines first and second fuel masses for first and second fuel injection systems of the engine, respectively, and that controls the first fuel injection system to inject a first fuel based on the first fuel mass. The second control module controls the second fuel injection system to inject a second fuel based on the second fuel mass. A second control system for an engine includes first and second control modules. The first control module controls a first fuel injection system of the engine to inject a first fuel and selectively disables at least one of a plurality of components of a second fuel injection system of the engine. The second control module controls the second fuel injection system to inject a second fuel.