Okay, anime subdomain is done, with the exception of a small layout change. I'm sure manta2g will get to that as soon as it is possible for her to do so.
In the meantime, for your stories that are now in top level categories, (i.e. categories where stories number 200 or more) which you now see in the side menu, you can actually edit the placement and put it where it belongs. Edit your story, and change the subcategory it's in to the subcategory it would actually belong to, and if there is a pair specific sub sub category where it would belong, you can select that as well.
Something to keep in mind, there are three categories which are NOT pair type specific, but STORY type specific. These would AU, Crossovers, and General. General should be for stories that aren't concentrated so much on a relationship, but on writing in that particular world. Just a general sort of story. AU, of course, would be any Alternate Universe stories. Crossovers are self explanatory
You can expect to see this subdomain by subdomain.