The Lodgix plugin is constantly being updated, thus you should never make changes to any of the php files provided in the plugin.
Custom CSS should be placed in a theme/child theme or in the customizers additional css panel.
At present there are some actions/hooks that can be customized in a themes functions.php file. In the future we will build out a template system similar to plugins like WooCommerce or Events Calendar Pro that gives developers a folder that they can drop into a theme and override templates there.
More details on customization capabilities will come out in June 2021.