New hybrid FPGA platforms that couple processors with a reconfigurable fabric, such as the Xilinx Zynq, offer an alternative view of reconfigurable computing where software applications leverage hardware resources through the use of often reconfigured accelerators. For this to be feasible, reconfiguration overheads must be reduced so that the processor is not burdened with managing the process. We discuss partial reconfiguration (PR) on these architectures, and present an open source controller, ZyCAP, that overcomes the limitations of existing methods, offering more effective use of hardware resources in such architectures. ZyCAP combines high-throughput configuration with a high-level software interface that frees the processor from detailed PR management, making PR on the Zynq easy and efficient.