While Network-on-Chip aspects such as topologies, routing strategies or Quality-of-Service have been largely studied, the mapping of real applications on distributed NoC-based architecture is still an open issue. In this paper, we address this issue for complex reconfigurable data-flow applications. We introduce the concept of Communication and Configuration Controller (CCC) which interacts both with the usual Network Interface and the IP core structure. The proposed CCC is a programmable template-based architecture, which provides solutions to manage reconfiguration flows, data synchronizations and global control signaling. An implementation of the CCC is presented, and its performances in a 65nm technology are discussed through a concrete telecommunication application.