The phpMyAdmin configuration settings are well documented via the Web GUI. IE, if you want to change a behavior, look for it in the GUI settings, click the question mark next to the item and it refers to the variable that controls the setting. It can then be changed in the /config.inc.php file. It's like they wanted to cut down on Googling for information on phpMyAdmin (that's a compliment). But then again, it would be even nicer if the changes made in the Web GUI were permanent. There's probably a per user setting file that can be configured, but it would be great to have a button in the GUI that says "Save your settings" instead of "Apply" and considering that one is logging in a specific user, this seems reasonable. Oh, well, its not perfect, but it is fairly great and better than doing complex stuff with the command line.
Navigation Tree Grouping: /usr/share/phpMyAdmin/config.inc.php (path if installing via YUM for CentoOS) add the following;
$cfg['NavigationTreeEnableGrouping'] = '0';