You need to create the subfolders on the USB that you use for it. PM me if you need any expert help, I have created a many, many RetroPi System.
Try and stick a random ROM into any folder and you will see the system up there. Here are the dumbed down instructions, after you take the USB out, it will create all the emulator folders, if you dont have a ROM in there, it wont show.
USB stick
Ensure that the USB stick is formatted to FAT32 or exFAT, and that the SD card has enough free space to hold all ROMs
Create a folder called retropie on the USB stick
Plug it into the RetroPie system. If the USB stick has an activity light, wait for it to finish blinking, else wait a few minutes
Remove the USB stick out and plug it into a computer
Add the roms to their respective folders (within the retropie/roms folder) * this is where you will see all the emulators that ver is capable of running
Plug it back into the RetroPie system. If the USB stick has an activity light, wait for it to finish blinking, else wait (with many GBs of ROMs, wait several hours)
Remove the USB stick, the ROMs have been transferred from the USB to the SD card
Refresh the game listing in Emulationstation by pressing F4, or choosing Restart Emulationstation/Restart System via the start menu
The transferred games should now be visible within Emulationstation. If any are missing, return to step 6