I followed qmailrocks exactly.
The site really isnt missing steps....
I dont enter my virtual domains in /etc/hosts, I let dns and apache take care of that.
As far as maildirs, which is the format i am using, they will be created in /home/vpopmail/domains/domainname/user/Maildir , you have to remember that everything is virtual now, so the Maildir will not be in the users home directory.
as far as setting up maildir all you have to do is put ./Maildir as the only line in /var/qmail/control/defaultdelivery.
When logging into squirrelmail with this setup a common mistake is that people don't realize that you have to login as 'firstname.lastname@example.org' not just as 'user'
I'm guessing that if you followed the guide that apache is set up correctly for virtualhosting.
If you are stumped contact me or post again, I can be contacted at email@example.com
and i'd be glad to take a look.
Hope this helps,