What are you talking about and where did you get your info? All of your ROMs can go in one folder. You can sub-divide them into categories or alphabetically if you like but that's entirely optional. If you are using that unofficial aksommerville version at the bottom of the WiiBrew page DON'T. It hasn't been updated in like 3 years and is junk. Use Tantric's official FCE Ultra GX v3.2.5.
If you need help check this guide out.