"I do not have many ROMs" is subjective 😉, but for your scenario it sounds like you should just leave them on the external. I think it mostly depends on the systems you're into. If your favorite systems are NES and Gameboy, you could easily store a complete collection on a very small internal drive. The point of LaunchBox is to build a beautiful looking library, so if you don't keep the external drive plugged in, it will be a library of dead links. Another option you might want to consider is installing LaunchBox itself to the external drive, and just make that your "gaming drive" and only play while it's plugged in.
e.g. if your external is drive E- you'd just run E:\LaunchBox\Launchbox.exe and put all your games in E:\LaunchBox\Games
Everything would be clean and contained in the LaunchBox folder.