Small-to-moderate sized commercial buildings commonly use rooftop units (RTUs) to provide indoor comfort. These applications are often characterized by significant spatial variations in comfort due to poor thermostat placement and poor coordination of RTUs leading to high energy and demand costs and marginal comfort. Tools are needed that can assess both energy and comfort performance for these types of applications so that the benefits of improved RTU coordination and control can be evaluated in terms of energy and comfort and so that appropriate real-time strategies can be developed. In the following we discuss a method for generating and coupling tractable reduced order models for the building envelope and for the indoor air dynamics. Overall assessments of the coupled model are being performed for a typical sit-down restaurant that employs four rooftop units. Measurements from the site are used to validate the models.