We consider a discrete manufacturing system with a mathematical representation in the form of a two-level model. The model defines the structure of a technological process in the form of a special two-stage scheduling problem. For the proposed new model of a discrete production system, we solve a management problem consisting of two interconnected subproblems of operational scheduling and operative operational planning. We present an original solution to the formulated problem of a discrete manufacturing system management. We substantiate an efficient software architecture, which includes a model for efficient static management of asynchronous computing processes. The management model is an organic consequence of the proposed method of managing a two-level discrete manufacturing system. We show that the efficiency of the proposed method and of the corresponding algorithms depends significantly on the efficiency of solving several single-stage scheduling problems, which were the object of the authors’ previous theoretical and experimental research. Finally, we give an illustrative example that confirms the practical value and efficiency of the proposed models and methods.