With the adoption of integration and system perspectives in managing the manufacturing systems and the pressure imposed by the increased competition and rapidly changing business environment, the need has arisen for new approaches for simulating the manufacturing enterprise. We have proposed SDDES; a hybrid System Dynamics Discrete Event Simulation approach to simulating the integrated manufacturing enterprise. SDDES offers comprehensive simulation models that encompass all management levels and recognize the differences between them in terms of scope and frequency of decision making as well as the levels of details preferred and used at each level. SDDES maintains the integrity of the two simulation paradigms and can use existing/legacy simulation models without requiring learning new simulation skills. In this paper we describe the modular structure of SDDES, our method to synchronize and coordinate SD and DES, and the functional model of the SDDES controller, which manages the integration of the two simulation methodologies.