Is there any way to to have phpmyadmin run on the Directadmin port? I don't like the idea of it being publically accessible right now and I know it's being done on cPanel.
You can't make it run on the DirectAdmin port, however you can set up a customized Apache vhost with a different port number so it's harder to find where it is. Doing so shouldn't be too much of a problem, there's plenty information on how to do it out there.
Once you have done that you'll want to modify the lines in httpd.conf that have something like this:
Alias /phpmyadmin /var/www/html/phpMyAdmin
Alias /phpMyAdmin /var/www/html/phpMyAdmin