This is driving me batty because I know I have this fic somewhere, or at least think I do.

Jared is a villain kinda person and his power is entropy/chaos.
In his civilian life he is in a relationship with Jensen.

Jensen is a hero and his power is order.

They are happy as boyfriends, don't know the other is their nemesis, but they do find out. But they both comment on how, once they figure it out, it made sense.
Jensen never wanted to stay at Jared's apartment because the chaos hurt him.
Jared didn't want to stay at Jensen's because the order and neatness hurt him.

They find their powers, somehow, work together and they find a happy compromise.

It's not Charades by Bertee, which is excellent and I suggest anyone read it.

Found by saltandburnboys: Opposites kink-meme fill - http://spnkink-meme.livejournal.com/67741.html?thread=22189213