Head back to the fort. Talk to Isran. After the rallying speech, you'll head for Volkihar castle. Be prepared because you're headed for Harkon's throne room. Make your way through the castle and up to the Cathedral. You'll have to cut your way through all the different vampires and hounds to get up there. This shouldn't be too difficult because you'll be accompanied by a rather large group of Dawnguard. Make your way up to the chapel. Harkon will be ready for a fight but he'll still want to talk first. You'll have the chance to hand him the bow but I suspect that he'll just try to kill you anyway, requiring you to kill him just the same. I say don't.
The battle will start. Use magic on him if you like, get close for melee. Do whatever you like to do damage. Watch out for the various minions he summons to fight with him. From time to time he will teleport around the room, making him a hard target for a melee. If you've got an abundance of Sunhollow Arrows, you can use those for some massive damage here. If not, hang on to them because they are useful for something else.
After you do some damage, he will move to the back of the room and form a shield around him. When he does this, shoot the Sunhollow Arrows at him with Auriel's Bow and it will destroy his shield. Once it's down, continue on with the battle as usual. Once he's killed, you will be recognized as the most powerful vampire and the Lord of the castle. This will allow you to take radiant quests from the Dawnguard here just like any other faction.
There's one more important thing that happens here. After the fight, Serana will offer to be your companion. This is very useful because she will allow you to use her blood with Elven arrows to make blood cursed arrows. If you shoot one of these at the sun, it will blot out the sun for the rest of the day (and grant you an achievement).
*Achievement: Kindred Judgment
*Achievement: Auriel's Bow