The installer script automatically creates configuration file for your server, but yes, you can customize some things BEFORE you run the installer. You can do that by creating install_defaults.php file in the main /privmx folder. The file will be used during the installation process and will overwrite default settings. Example content of the install_defaults.php file:
"databaseEngine" => "qdbm",
"dataDirectory" => "/some/custom/directory/for/your/secrets"