Module configuration page
Basic and the most important configuration section of pretty clean urls is located on module configuration page. Here you can control from what pages module will remove the ID. PrestaShop has several types of pages and each of these pages can have ID or not, for example: category pages, product pages, cms pages, cms category pages, suppliers, manufacturers.
Clean urls and multistore feature
Multistore feature in PrestaShop is great feature to build many shops that can be controlled from one back office. This means that with this feature, you can manage many customized shops, which share many common elements. For more efficiency, you can even create groups of shops etc. Each of this shop can have own unique configuration and unique modules that are enabled. Pretty clean urls module fully supports multistore configuration, but in this case - it requires to configure it carefully.