A method to control an exhaust gas recirculation and a manifold air pressure in an engine includes utilizing a decoupling matrix within a multiple input and multiple output controller to determine an exhaust gas recirculation command and a manifold air pressure command, wherein the decoupling matrix is configured based upon a diagonally dominant model of the engine compensated by the determined exhaust gas recirculation command and the manifold air pressure command. The exhaust gas recirculation and manifold air pressure are controlled based upon the determined exhaust gas recirculation command and the determined manifold air pressure command.