When you go into "Re-Order Forums", the subforums will be listed in with it. It's a bit confusing (and it will get better in a couple of releases), but you can just move the subforum up or down, and if it's above or below other subforums in the same forum, it'll turn out that way. That's probably really confusing...
Like, you have:
--------> Subforum 1
--------> Subforum 2
--------> subforum 3
etc. If you want to have Subforum 2 where Subforum 1 is, you can just move it upwards one, so it's above Subforum 1. And it'll stay that way when it's in the forum.
Let me know if that made any sense whatsoever....