The Lodgix plugin is constantly being updated, thus you should never make changes to any of the php files provided in the plugin.
To modify the plugin CSS, create a file and name it: lodgix-custom.css
This file should be placed in: /wp-content/
Any css present on directory.php can now be overridden using the file: /wp-content/lodgix-custom.css.
Remember, lodgix-custom.css must have exactly that name and must be located in /wp-content/.
The custom.php (or whatever name you choose, as it's configurable within the plugin settings) file is meant to solve issues related to Wordpress themes and pages. For example, some themes/configurations require footer in different places, or with no sidebars, etc.