If you have enable Front Page extensions, which I believe that you do, you can't access your site VIA FTP. When dreamhost sets up your domain to work with front page extension it changes the permissions on all of your files so that you can't access them through the normal means. you won't see any of your files that you publish through front page on FTP or though shell access, but they're there.
Dreamhost also doesn't make the same automatic backups that they do for normal domain. so be sure and keep copies of your site on your own computer.
I have a domain set up with frontpage extension... not really great. Also if you don't want to publish your site through front page, you don't really need frontpage extension turned on, you don't need them enless you're using a frontpage submit form, or discussion pages. (and thoes can be replaces with easly aviable dreamhost scripts)