There are multiple options for setting up your permalink structure with the plugin. Read this page about how to setup the url structure in WooCommerce.
You can choose between multiple options:
Option number 1:
full path: webshop.com/category/sub-category/product
This means that the product and categories will all show up in the url structure. This can be good for your link structure.
Option number 2:
full path + base: webshop.com/store/category-subcategory/product
In some cases you would also like to have a ‘base’ in your url structure. Sometimes this has to be done when migrating from Magento to WooCommerce for instance.
Option number 3:
full path + suffix: webshop.com/category/sub-category/product.html
Option number 4:
single product: webshop.com/product
Option number 5:
all categories minus product: webshop.com/category/sub-category
Option number 6:
deepest category + product: webshop.com/sub-sub-category/product