Right now, what you can do is create the subsite directories under www/subsite-name/ and put a resources directory underneath it for each subsite.
I am thinking that ideally we do want to put subsite templates under site-root/templates/ and build a corresponding cr_folder structure. Then with optional WebDAV support, or through a web interface, the ADPs could be edited for each subsite, and published back to the filesystem.
This doesn't help you right now, but it is good to think about how it might work better.
