If you would like any customised changes to the default PHPMyAdmin setup on your server, the best thing to do is to install PHPMyAdmin directly within one of your servers cpanel accounts and make the changes in that version.
This is due to your servers main PHPMyAdmin configuration being over-written nightly with the server updates and patches, and things such as changes to the config.inc.php file and other such tweaks will all reset back to the defaults each night.
