In the context of automated manufacturing systems, flexibility and synchronization are two main representative formations. Supervisory control techniques for flexibility have gained increasing attention, but those for synchronization operations have received little notice. Based on their comparison, our work makes threefold contributions. First, we propose a novel characterization of siphons, i.e., type I and type II, based on a special kind of Petri nets, namely, hierarchical augmented marked graphs (HAMGs), which integrate multilevel synchronization into a system. This characterization of siphons is further proved to be a crucial and essential description for both synchronization and flexibility. Second, event circular-wait is proposed to describe the occurrence of deadlocks in HAMGs. Its counterpart is resource circular-wait in flexibility. Ours is a more general and accurate characterization of deadlocks. The liveness of HAMGs can be attributed to the absence of undermarked siphons. Third, a unified liveness-enforcing supervisory control is established based on new characterization of siphons with the aid of generalized mutual exclusion constraints. Supervisor simplification based on inequality analysis is provided for structure simplicity. An experimental study illustrates the correctness of such characterization and the effectiveness of our proposed control method.