Well, the easiest thing would be to just run MESS on a PC. 
It's all pointless nostalgia tech in the end, so there's not really a right or wrong way to do it, but I personally don't want to use an emulator. Running compiled C code on a general purpose CPU seems little different to me whether it's a PC's Core i7 or an ARM chip on a custom board. I really want to implement things at the hardware level, using a real CPU, with the FPGA replacing peripheral chips like the VIA and SCC. I've made some decent progress down that path so far, though there's still a long way to go!
It's all pointless nostalgia tech in the end, so there's not really a right or wrong way to do it, but I personally don't want to use an emulator. Running compiled C code on a general purpose CPU seems little different to me whether it's a PC's Core i7 or an ARM chip on a custom board. I really want to implement things at the hardware level, using a real CPU, with the FPGA replacing peripheral chips like the VIA and SCC. I've made some decent progress down that path so far, though there's still a long way to go!