Dark Ganon is a semi-boss that you first fight in the Forsaken Fortress, just hit all of his attacks back at him, he'll try to rebound them but if you just keep swinging at the right time, you should do fine. After he falls to the ground, you can hit him. You fight him again in Ganon's Tower in which case when your in the room with the blue floor panel and you get the chance you should hit him with the light arrow.
There are several strategies you can use to beat a dark nut, you can try hacking away at it's armor until it breaks, you can wait til you get a chance to hit it in the back to drop off it's armor or you can use parry attacks to knock of it's armor and helmet. However, whatever method you use will end usually end up in a sword fight, lest you use some other weapon to attack his exposed body.
This is the form Ganon takes to test if you are really the Hero of Time. He starts off as a large marionette in which case you simply break off his green strings and hit the blue ball with a light arrow. His next form is a spider, he'll spin around for awhile and then drop down to the ground where you can easily hit him with a light arrow by simply hookshotting to one of the flame posts. Finally, his last form is that of a millipede, just shoot his blue ball with a light arrow when the chance arrises or stun him with a bomb. When he's destroyed Ganon will reveal that he was pulling the strings.
These enemies are always prove to be some of the most difficult in the Zelda series. In the Wind Waker, they are almost impossible to stun, and therefore the easiest way I've found to beat them is to use the hurricane spin and when it splits in two destroy the legs first, then the upper body, and finally slash away at the head before it reforms. If you haven't learned the hurricane spin, your best bet to beating it without losing hearts is by using bombs to blow it's body up, then use the same strategy on the head.