1. A method for designing a system on a target device, comprising: distributing a timing budget for generating a netlist for a first partition; merging the netlist for the first partition of the system generated from a first design flow of a first type with a netlist for a second partition of the system generated from a second design flow of a second type to form a combined netlist; and performing fitting on the combined netlist, wherein the distributing, merging, and performing is implemented by a processor.