Modern multiprocessor systems-on-chip (MPSoCs) are expected to handle multi-application usecases. As the number and complexity of these applications scale, resource allocation to meet the application throughput requirement is becoming quite a challenge. In this paper, a complete design flow is proposed for partially reconfigurable heterogeneous MPSoC platforms. The proposed flow determines the minimum resources required to map and guarantee the throughput of applications in all use-cases. Further, a suitable mapping for each application is chosen so that energy consumption is minimized. Experiments conducted with a set of synthetic benchmarks and real-life applications clearly demonstrate the advantage of our approach over homogeneous or fully reconfigurable designs. The proposed design flow achieves more than 50% energy savings when the number of configurations is not optimized. With configuration-optimization, our flow results in 75% reduction in the number of configurations with 5% reduction in energy.