This interesting paper from Intel explains how they got a FPGA-based Atom processor running in a regular PC.
It gives some insight about how a modern processor is designed (entirely in SystemVerilog), how it could be ported to FPGA (including a lot of practical aspects), and about the debugging and testing phases (on real PC hardware).
“Once the netlist is produced by DC-FPGA, Xilinx ISE 10.1.03 is used to produce the final bitfile. However, it turns out that DC-FPGA in rare occasions can produce buggy netlist silently, even for a correctly developed RTL circuit that passes the RTL simulation”
“Though these behavioral RTL models can be naively passed to the logic synthesis tools which may sometimes infer appropriate FPGA-specific memory structures, for most structures we observed an explosion in LUT utilization.”