Implementing self-adaptive embedded systems, such as UV, involves an offline provisioning of the several implementations of the embedded functionalities with different characteristics in resource usage and performance in order for the system to dynamically adapt itself under uncertainties. FPGA-based architectures offer for support for high flexibility with dynamic reconfiguration features. We propose an autonomic control architecture for self-adaptive and self-reconfigurable FPGA-based embedded systems. The control architecture is structured in three layers: a mission manager, a reconfiguration manager and a scheduling manager. In this paper we focus on the design of the reconfiguration manager. We propose a design approach using automata-based discrete control. It involves reactive programming that provides formal semantics, and discrete controller synthesis from declarative objectives.