When configuring the custom catalog, you have to. make sure to configure the appId to point to your custom collection. That’s likely the missing piece.
See this tutorial, it’s no. 10 in step 1 - it tells you how to get and then set the new app id for the custom catalog. https://support.wix.com/en/article/velo-tutorial-ecommerce-catalog-custom-extension-beta
Once it’s pointing to your catalog, the add to cart functionality is automatically pointing to those items instead of the regular product collection