I think the easiest way is to put the Good Tool into the same folder with your ROMS. Then open up the command prompt and run the Good Tool but put "rename forcexbox" at the end. For example, if you were going to rename your SNES ROMS you would type this: "\path\GoodSNES.exe rename forcexbox"
It will then rename and put all the ROMS it recognized into a sub folder and produce text documents telling you every ROM you have and every ROM you are missing.