If you want a virtual site without the 'www' in front, create it like you would a normal site, except as email server + web server alias fill in "domain.ext" as well.
Then you need to ssh in to the machine, and in /home/sites/ add a link to domain.ext (ln -s /home/sites/siteXX /home/sites/domain.ext)
edit /etc/httpd/conf/httpd.conf
and change the following:
RewriteCond %{HTTP_HOST} !^domain.ext(:80)?$
RewriteRule ^/(.*) http://domain.ext/$1 [L,R]
RewriteOptions inherit
AliasMatch ^/~([^/]+)(/(.*))? /home/sites/domain.ext/users/$1/web/$3
(there should have been a 'www' before 'domain.ext' or whatever you filled in as 'host name' in the administrator)
Then you need to do the same for the sitemanager
ln -s /usr/admserv/html/.cobalt/siteManage/siteXX /usr/admserv/html/.cobalt/siteManage/domain.ext
(don't need to edit the /etc/admserv/conf/httpd.conf!)
As far as I remember you don't need to change anything in the mail aliases database...