Different formalisms and modeling frameworks have been developed to capture the discrete behavior of manufacturing systems. However a purely discrete model does not capture the continuous variables of machine-level operation. Previous research in modeling manufacturing systems has studied the quantity-quality and quantity-reliability coupling of production environments but their relationship to energy consumption is often not considered. This work presents a framework that extends the state-of-the-art in modeling manufacturing systems to support decision making for control at both machine- and system-level variables using hybrid models. The modeling strategy considers the coupling between productivity, quality, reliability and energy consumption and leverages the current plant floor data extraction capabilities to develop data-driven models. A novel control strategy is presented that considers the effect of various machine- and system-level variables over different performance metrics and balances them using multi-objective optimization. This framework was validated using a combination of real and simulated data of a production representative environment. The optimal set of control variables is obtained using simulation-based optimization to support plant floor decision making by studying process variables, maintenance actions, or system reconfiguration. Results show the effect of different control variables and the ability to reduce energy consumption while improving productivity. The implementation of the modeling and control framework presented here has the potential to impact the operations of manufacturing system by reducing cost and improving productivity.