Scheduling in a stochastic network is an issue in many applications such as the workflow on production shop floors, automated service operations on internet platforms, traffic coordination in guidepath-based transport systems, and resource allocation in multi-core computer architectures. It is an area of the modern scheduling theory with very limited results. To a large extent, the lack of results is due to the intricacies that arise from the blocking and deadlocking effects that take place in these networks which prevent analysis using classical modeling frameworks. These type of scheduling problems can be resolved by breaking them into a supervisory control problem that seeks to prevent the deadlock formation in the underlying resource allocation dynamics, and a scheduling problem formulated on the admissible subspace to be defined by the adopted supervisory control policy. Logical Control of Complex Resource Allocation Systems provides a comprehensive tutorial on solutions to the supervisory control problem. The reader is shown results that are theoretically rigorous yet offer rich practical applications. These resource allocation techniques have major implications for many modern-day and future applications. They also point the way forward for the necessary further research to successfully solve the scheduling problems in such systems. This is a comprehensive introduction for students, researchers, and practitioners into a significant development at the core of many control systems.