Yeah, that seems to be the way its working. Forums that you check “Forum is Category” for become container forums with no topics and special CSS classes. I think that’s a fine way to do it once you understand what’s going on. It just seemed a bit weird at first because in the backend there isn’t really any differentiation between category forums and regular forums.
In order to accomplish what you want, with the positions of different forums laid out differently you are going to have to modify your front-page template file pretty heavily.
You’ll want to modify the ‘<?php if ( bb_forums() ) : ?>’ section so that it positions each forum in a different area of your page as it goes through the loop. It will likely get pretty tricky as you try to get the subforums underneath the parent forums since they may or may not be in that order in the loop.