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: DownCityOutfitters.com
This will then assign items under this DownCityOutfitters.com category tree to the website downcityoutfitter.com 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: