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This paper addresses the challenge of controlling an overactuated engine thermal management system where two actuators, with different dynamic authorities and saturation limits, are used to obtain tight temperature regulation. A modular control strategy is proposed that combines model predictive control allocation (MPCA) with the use of an inner loop reference model. This results in an inner loop controller that closely matches a dynamic specification for input-output performance while addressing actuator dynamics and saturation constraints. This paper presents the design and implementation strategy and illustrates the effectiveness of the proposed solution through real-time simulation and experimental results.