An engine includes an exhaust gas recirculation system with a high pressure exhaust gas recirculation loop and a low pressure exhaust gas recirculation loop, and an air charging system. A method of controlling the air charging system includes monitoring an actual exhaust gas recirculation rate, operating conditions of a compressor and turbine in the air charging system. A compressor flow is determined based on a target exhaust gas recirculation rate, a target intake manifold pressure and the actual exhaust gas recirculation rate. A power requested by the compressor is determined based on the compressor flow, the target intake manifold pressure, and the monitored operating conditions of the compressor. A power to be generated by the turbine is determined based upon the power requested by the compressor. A turbine flow is determined based upon the power to be generated by the turbine and the monitored operating conditions of the turbine. A system control command is determined based on the turbine flow and the monitored operating conditions of the turbine. The air charging system is controlled based on the system control command.