Increasingly System-On-A-Chip platforms which incorporate both microprocessors and re-programmable logic are being utilized across several fields ranging from the automotive industry to network infrastructure. Unfortunately, the development tools accompanying these products leave much to be desired, requiring knowledge of both traditional embedded systems languages like C and hardware description languages like Verilog. We propose to bridge this gap with Twill, a truly automatic hybrid compiler that can take advantage of the parallelism inherent in these platforms. Twill can extract long-running threads from single threaded C code and distribute these threads across the hardware and software domains to more fully utilize the asymmetric characteristics between processors and the embedded reconfigurable logic fabric. We show that Twill provides a significant performance increase on the CHStone benchmarks with an average 1.63 times increase over the pure hardware approach and an increase of 22.2 times on average over the pure software approach while reducing the area required by the reconfigurable logic by on average 1.73 times compared to the pure hardware approach.