Aspects of the disclosed technology relate to techniques of design implementation for FPGA prototyping. An initial FPGA-mapped netlist and a generic RTL design associated with the initial FPGA-mapped netlist are generated based on an original RTL (register-transfer level) design for a circuit design and optionally on verification-related features. Based on the initial FPGA-mapped netlist, the circuit design is partitioned into design partitions for implementing the circuit design across a plurality of FPGA chips. Final FPGA-mapped netlists are then generated based on the design partitions represented by the generic RTL design or by a combination of the generic RTL design and the initial FPGA-mapped netlist.