Ah, why didn't you just say that xD
You need to start the timer when you save your time setting. When you did, turn your DS off and on again, and wait until the first timer is going to run out. When it reaches 0, make sure you click your game at the very same time. Then, the second timer will be running. Keep pressing A until you reach the Continue screen. There, you have to wait until the second timer runs out. Again, when this timer hits 0, you have to enter your game at the exact same time. Then you have to verify your seed (Elm Calls (HGSS), Coin Flips (DPPt)) to see which delay you've hit.