An engine assembly includes an engine and a plurality of actuators. The plurality of actuators includes a first turbine serially connected to a second turbine, the first turbine being a relatively high pressure turbine and the second turbine being a relatively low pressure turbine. A controller is configured to transmit respective command signals to the plurality of actuators. The controller is programmed to obtain respective transfer rates for the plurality of actuators based at least partially on an inversion model. The controller is programmed to control an output of the engine by commanding the plurality of actuators to respective operating parameters via the respective command signals. Prior to obtaining the respective transfer rates, the controller is programmed to determine a respective plurality of desired values and respective correction factors for the plurality of actuators.