This paper examines a method for real-time control of non-inductively sustained scenarios in NSTX-U by using TRANSP, a time-dependent integrated modeling code for prediction and interpretive analysis of tokamak experimental data, as a simulator. The actuators considered for control in this work are the six neutral beam sources and the plasma boundary shape. To understand the response of the plasma current, stored energy, and central safety factor to these actuators and to enable systematic design of control algorithms, simulations were run in which the actuators were modulated and a linearized dynamic response model was generated. A multi-variable model-based control scheme that accounts for the coupling and slow dynamics of the system while mitigating the effect of actuator limitations was designed and simulated. Simulations show that modest changes in the outer gap and heating power can improve the response time of the system, reject perturbations, and track target values of the controlled values.