Modularity is a fundamental feature of real networks, being intimately bounded to their functionality, i.e., to their capability of performing parallel tasks in a coordinated way. Although the modular structure of real graphs has been intensively studied, very little is known on the interactions between functional modules of a graph. Here, we present a general method based on synchronization of networking oscillators, that is able to detect overlapping structures in multimodular environments. We furthermore report the full analytical and theoretical description on the relationship between the overlapping dynamics and the underlying network topology. The method is illustrated by means of a series of applications.