http://www.directadmin.com/forum/showthread.php?t=198
Although ~username/domain.com will be the new default, for existing systems, if you wish to use the standard ~username method still, you can add:
old_public_html_link=1
to your directadmin.conf and the old fashioned way of handing the link is used.
The internal default will be:
old_public_html_link=0
which won't be present in the directadmin as it's the internal default.
This change will convert the link:
/home/username/public_html
to a directory, and links for each domain will be placed inside that.
Note that existing users will not be affected until they do something domain related, like add another one, change the name, or change their default domain.
If they don't touch anything then the link will remain untouched.
Inside the new /home/username/public_html directory will be an .htaccess file.
This .htaccess file will be created via a template in:
/usr/local/directadmin/data/templates/userdir/.htaccess
You can override this with a custom version, but creating:
/usr/local/directadmin/data/templates/custom/userdir
and putting whatever you want in it.
Anything in the priority userdir directory is fully template/parsed (see the .htacess for an example)