Systems based on Xilinx Virtex series FPGAs can benefit, compared to traditional rad-hard technologies, from high performance, high logic density and dynamic reconfiguration capability. However, the underlying SRAM technology is sensitive to ionizing radiation, which can induce faults that must be managed to improve system's dependability. This paper proposes a Dual-Layer Fault Manager concept, which aims at managing both configuration and application faults, dynamically balancing redundancy level, dependability and functionality. This concept has been prototyped and its initial test results are discussed.