The built in media server only supports that small set of folders for sharing: http://www.microsoft.com/windows/products/winfamily/windowshomeserver/share.mspx.
There may be some way around this. Alternatively, you could use an add-on media server like TwonkyMedia Server. I don't think it's supported by Twonky just yet (except the MediaSmart version), but there are others who have used it successfully.
The other option would be just to move your media to the default folders. I'm guessing you're not interested in that, but it is an option. If the goal is to keep your stuff separate from your roommates stuff, you could always just create sub folders for each person.
Good luck, hopefully you can figure out something that works well for you.