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Field Programmable Gate Arrays (FPGAs) have long held the promise of allowing designers to create systems with performance levels close to custom circuits but with a softwarelike productivity for reconfiguring the gates. Unfortunately achieving this promise has been elusive. Modern platform FPGAs are now large enough to support complete heterogeneous Multiprocessor System-On-Chips (MPSoCs), however standardized design flows and programming models for such platforms do not yet exist. To achieve true softwarelike levels of productivity, the design flow and development environment for heterogeneous MPSoCs must resemble that of standard homogeneous systems. In this paper we present a new design flow and run-time system that enables developers to program a heterogeneous MPSoC using standard POSIX-compatible programming abstractions. The ability to use a standard programming model is achieved by using a hardware-based microkernel to provide OS services to all heterogeneous components. This approach makes programming heterogeneous MPSoCs transparent, and can increase programmer productivity by replacing synthesis of custom components with faster compilation of heterogeneous executables. The use of a hardware microkernel provides OS services in an ISA-neutral manner, which allows for seamless synchronization and communication amongst heterogeneous threads.