They can be put into any number of folders anywhere on your card except the __aio folder. What I did was create a folder called DS on the root and within that folder created several more for the different types of games (eg. Action, RPG, Puzzles, Adventure, etc.). This way, it speeds up load times when you browse your games. When you have all your games in one folder, it may take a while to show up when you open that folder.