You shouldn't need to create manually any folders, they are created (with the correct name) when the corresponding emulator is installed. RetroPie already comes with emulators installed, so the basic folders should be already present.
The thing is these folders aren't appearing on my SD card that had Retro Pie on it.
If you're looking at the SD card's contents on a Windows PC, you will only see the boot partition, the 2nd partition holds the actual system (and the RetroPie installation), but Windows doesn't know how to read the Linux filesystem on it - so you won't be able to see the folders.
So, if I were to create folders manually, where would I create them on the USB?
No, you don't need to create the folders manually. If you want to transfer your ROMs over, take a look at the Docs. If your RetroPie system is connected to your network, the easiest method for transfer is via File Shares from your PC.