1. A non-transitory computer readable medium including a sequences of instructions for causing a processor to execute a method comprising: partitioning a system into a first partition and a second partition; assigning a timing budget for each partition; processing the first partition independently from the second partition using a bottom-up design flow without a top-down design flow to generate a post-synthesis netlist for the first partition; processing the second partition using a top-down design flow without a bottom-up design flow to generate a post-synthesis netlist for the second partition; merging the post-synthesis netlist for the first partition and the post-synthesis netlist for the second partition to form a combined netlist; and performing fitting on the combined netlist by placing functional blocks of the system on a target device and connecting the functional blocks with routing resources on the target device.