phpMyAdmin has quite a lot of configuration settings, those are described in config. There are several layers of the configuration.
The global settings can be configured in config.inc.php as described in config. This is only way to configure connections to databases and other system wide settings.
On top of this there are user settings which can be persistently stored in linked-tables, possibly automatically configured through zeroconf. If the linked-tables are not configured, the settings are temporarily stored in the session data, these are valid only until you logout.
You can also save the user configuration for further use, either download them as a file or to the browser local storage. You can find both those options in the Settings tab. The settings stored in browser local storage will be automatically offered for loading upon your login to phpMyAdmin.