The stratification of Internet protocols segregates network functionality into two broad layers: the overlay layer (application level) and the underlay layer (network level). Overlay networks are typically not aware of the operation of underlay networks, and conversely underlay networks are blind of the services executing at the overlay layer. Even though there is a prolific deployment of overlay networking based services, this architectural design is proving to have a number of deficiencies. Typically, such services make poor use of underlying networking resources, leading to degraded user-perceived quality of service. We propose a two-layer coordination and control framework aimed at optimizing network performance and enhancing user-perceived service. The framework and corresponding middleware structure make use of active networking technology. We choose peer-to-peer systems as our overlay study case, and discuss the problems associated with providing two-layer optimization and application support for such systems. Finally, we draw conclusions about the potential benefits of this approach and point towards possible directions of future work.