I can't figure it out.

You have to revisit the Underforge area in Whiterun.

Ok thanks

http://www.uesp.net/wiki/Skyrim:Totems_of_Hircine

If you're talking about the new ones that came with the DLC, then (if it's at all similar to the Vampire Lord) the howls you have unlocked will be in your favorites when you transform into a werewolf (D-pad).

If you're NOT talking about the new ones, then you have to do side quests for Aela the Huntress AFTER you've completed the companions story. She will give you (eventually) quests to go retrieve werewolf totems, with which you can change your shout to various different effects (think there are 3, one that is your basic fear, one that is an advanced fear, and another that summons two spectral wolves to fight alongside you).

So I have to finish the companions quest line before I can even use the perks I unlocked for my werewolf form?

Not sure on that one. Probably not.

Those totems of Hircine were there before the DLC. I have yet to play through on a werewolf character, so I'm not totally sure how it all works.

Not sure on that one. Probably not.

The totems of Hircine were there before Dawnguard came out, so I would imagine you don't need to get them to get the perks (as it's a totally separate thing). However, I haven't played through on a werewolf character yet, so I'm not totally sure how that all works.

EDIT - sorry for the double post - something strange happened with my browser O.o

From what I've heard werewolves are still required to switch howls through the totems of hicrine (fear, summoning, life sense) they can't swap on the fly like vampire lords. Which is stupid I know.

Even with the perks? That seems strange.