Thanks for your attempts to help, but it really has nothing to do with the issue. I know where the paths are, and I'm using nginx anyway. I was just commenting that everything was working on my setup with a primary and a few add on domains, then I installed a StartSSL cerificate, and the next add on domains I added were pointing to the primary domain location. Files were in the correct spot, directories were created just fine. They just weren't going there. I ooked through error logsf for a clue, and saw something about certs in there, can't really remember what now it was awhile ago.
I uninstalled the ssl cert, and it all started working fine. So I got the sites working but it didn't really solve anyhing because I did want an ssl other than self signed for email. I'm taking care of that by hosting my email through a 3rd party site, so it doesn't affect me and I don't have to try to make it work.
Now that Let's Encrypt has gone public beta, I will mess with that just to give myself something to do, and if there are any things particular to installing them on Webuzzo I'll probably make a post here about it.