Methods and systems of controlling a dual fuel engine with at least two banks of cylinders are provided. The method may include sensing at least one of temperatures of exhaust from the at least two banks and a pressure of an intake manifold of the at least two banks, and adjusting at least one of a gas flow, a charge flow, or an air flow to one of the at least two banks to balance one of exhaust temperatures of the at least two banks and intake manifold pressures of the at least two banks.