A major modification made recently to the DIII-D tokamak was the rotation of one of the four neutral beam systems to allow injection of power in the opposite direction of the usual plasma current (counter-injection). Mixing the usual co-injection beams with the counter-injection beams provides a new capability that allows, for the first time, a partial decoupling of the injected energy and momentum during neutral beam heating experiments. To implement this capability, we have developed within the plasma control system (PCS) [B.G. Penaflor, et al., Fusion Eng. Design 71 (2004) 47] a model-based control algorithm for simultaneous regulation of plasma rotation and beta. The present work describes the development of the model, discusses its validation using actual experimental data, and presents the details of the implementation of the model within the PCS to allow simultaneous control of both plasma rotation and stored energy.