Hi! First of all you must be careful with autocopy function. This searches on the folder “roms” of the usb for new roms (if that folder doesn’t exist it’s created), and if there are new roms, it will copy them to the sd. You can deactivate it, or you can leave this folder empty and create other folder with your roms (games for example).
Ok, you have the games in a folder, now you need to modify this file:
How can you reach this file? you can use ssh or you can use an ftp (filezilla for example). I recommend you installing an ftp, it’s easy to manage files with it. If you have the usb plugged, you will see your folders in “/media/usb0/” if not, you have something wrong.
In this file you can disable emulators, and change the roms folder. You only need to change roms folder for each emulator like this:
“/Retropie/roms/mame/” change for “/media/usb0/games/mame/” for example.
If you scrapped the roms (It means that your games have picture and information), you need to modify gamelist.xml of each emulator. Change roms and image folders.
I think that I don’t forget anything, but feel free to ask.