One promising path for reducing the power consumption and improving the performance of building HVAC systems involves the coordinated design and operation of individual subsystems. This objective requires careful consideration of the dynamic interactions between the subsystems serving the occupied spaces. We propose a physical model-based approach for evaluating, optimizing, and designing control algorithms for integrated collections of subsystems to achieve high overall system performance. This approach is used in this paper to optimize the setpoints of and design dynamic controllers for an overall HVAC system consisting of a dedicated outdoor air system (DOAS) and a variable refrigerant flow (VRF) system serving a large occupied space. By optimizing the system inputs, we demonstrate that the energy consumption can be reduced by 15% as compared to the system with non-optimized inputs, and that nonintuitive system dynamics can be managed through systematic control analysis and design.