I'm wondering the way i would start establishing the virtual hosts to ensure that I have to enter www.mydomain.com:9090 to visit phpmyadmin. This is the way I've my vhosts setup at this time in httpd.conf:

<VirtualHost *:80>
    DocumentRoot /var/www/html/
    ServerName mydomain.com
    ServerAlias www.mydomain.com
</VirtualHost>

<VirtualHost *:9090>
    DocumentRoot /usr/share/phpMyAdmin/
    ServerName mydomain.com
    ServerAlias www.mydomain.com
</VirtualHost>

This doesn't appear to become working.

Perhaps you have attempted adding... Listen 9090 for your config?