A two-stage air charging system for an internal combustion engine with mixed exhaust gas recirculation includes a high pressure exhaust gas recirculation loop, a low pressure exhaust gas recirculation loop, an air throttle system, a turbo air charging system, and an electric air charging system. A method to control the system includes monitoring desired operating target commands and operating parameters. Feedback control signals are determined based upon the monitored desired operating target commands and the monitored operating parameters. The two-stage air charging system is controlled based on system control commands for each of the high pressure exhaust gas recirculation loop, the low pressure exhaust gas recirculation loop, the air throttle system, the turbo air charging system and the electric air charging system.