You must have the running boots for this to work. Go to the library just before the beach in Mabe Village. You'll see a book on the shelf, ram the shelf using the boots and read the book. It will tell you to go to the area in the graveyard with 5 tombstones. Be sure to memorize which order to push the tombstones in and what direction to move them in. It may take a few tries but if it's done properly a hole will appear leading you to the secret dungeon.