How to drain the well with the Song of Storms
Solution 1:
You need to enter the windmill in the back of Kakariko Village and pull out the Ocarina of Time in front of Guru-Guru as adult Link to learn the Song of Storms.
From Zelda Wiki:
In Ocarina of Time, the Windmill Man stands inside the Kakariko Windmill playing his Phonograph. If adult Link pulls out his Ocarina of Time in front of him, he will teach Link the "Song of Storms." If young Link plays the song inside the windmill, it will start spinning really fast, draining Kakariko's well and opening the way to the Bottom of the Well.
In order to become adult Link, simply continue following the story. Shortly after the third dungeon, you'll receive the Master Sword from the Temple of Time and become an adult.
You don't actually need to drain the well until much later in the game, though. The natural order of gameplay involves entering the Bottom of the Well shortly before the seventh dungeon.
As for the Gamecube Ocarina controls, the A button is still the same and the C-stick can be used in place of the C-buttons. You can also use Y as left-C, X as right-C, and Z as down-C. You can find more information on controls on StrategyWiki.
Solution 2:
Let the game progress naturally. I can't tell if your question is a result of too much or too little walkthroughs, but either way you should relax and just play the game following the plot. If he doesn't know how to become an adult he doesn't need the song.
Song of storms is integral part of the story, you can't miss it.
Becoming an adult is integral part of the story. You can't miss it.
If you don't know how to progress the story listen to what Navi, your fairy is saying. All will come in due time.