Launching in command line is the way GameEx works. Only other way to get Final Burn Evolution to work is to create a wrapper. As far as differences, Yes there are some. Final Burn Alpha supports more games. As far as exact differences I haven't compared the 2 exactly to see in detail but when I scanned my Final Burn Alpha roms in Final Burn Evolution, there were only a few that were not working only cuz they weren't built for it.