Honestly, you shouldn't have to create any directory structure; your loader should create the appropriate directories for you. Are you trying to move all of you SD contents to a USB drive?
I am not sure about GC games, but I have my hard drive in FAT32 format, which holds all my games, HBC APPS, etc. SD card is not required at that point. If you're going to move your SD card to the USB drive, then structure is the same (basically drag and drop from the SD card), other than that you should be good to go.