The Commerce5 product upload supports uploading products to multiple Magento websites. In order to have a different Ecommerce category tree for each website multiple root level categories must be created in Counterpoint as follows.

Create a root level category where the category name matches the website name EXACTLY as it appears in the product upload control as seen here:

Root Level Website Category:

This will then assign items under this category tree to the website in the Counterpoint Ecommerce Categories table as seen here:

You can now build our your full ecommerce category tree under each root level website category: