The electrification of engine components offers significant opportunities for fuel economy improvements, including the use of an electrified turbocharger for engine downsizing and exhaust gas energy recovery. By installing an electrical device on the turbocharger, the excess energy in the air system can be captured, stored, and re-used. This new configuration requires a new control structure to manage the air path dynamics. The selection of optimal setpoints for each operating point is crucial for achieving the full fuel economy benefits. In this paper, a control-oriented model for an electrified turbocharged diesel engine is analysed. Based on this model, a structured approach for selecting control variables is proposed. A model-based multi-input multi-output decoupling controller is designed as the low level controller to track the desired values and to manage internal coupling. An equivalent consumption minimization strategy is employed as the supervisory level controller for real-time energy management. The supervisory level controller and low level controller work together in a cascade which addresses both fuel economy optimization and battery state-of-charge maintenance. The proposed control strategy has been successfully validated on a detailed physical simulation model.