This study investigates the software automation and control framework for the MMT thermal system. Thermal-related effects on observing and telescope behavior have been considered during the entire software development process. Regression analysis of telescope and observatory subsystem data is used to characterize and model these thermal-related effects. The regression models help predict expected changes in focus and overall astronomical seeing that result from temperature variations within the telescope structure, within the primary mirror glass, and between the primary mirror glass and adjacent air (i.e., mirror seeing). This discussion is followed by a description of ongoing upgrades to the heating, ventilation and air conditioning (HVAC) system and the associated software controls. The improvements of the MMT thermal system have two objectives: 1) to provide air conditioning capabilities for the MMT facilities, and 2) to modernize and enhance the primary mirror (M1) ventilation system. The HVAC upgrade necessitates changes to the automation and control of the M1 ventilation system. The revised control system must factor in the additional requirements of the HVAC system, while still optimizing performance of the M1 ventilation system and the M1's optical behavior. An industry-standard HVAC communication and networking protocol, BACnet (Building Automation and Control network), has been adopted. Integration of the BACnet protocol into the existing software framework at the MMT is discussed. Performance of the existing automated system is evaluated and a preliminary upgraded automated control system is presented. Finally, user interfaces to the new HVAC system are discussed.