The EYEMAGINE HubSpot Magento Connector was originally designed to be used as a one-to-one implementation: 1 connector would link your HubSpot portal to one storefront and it's respective Magento backend.
The connector is capable of segmenting multiple storefronts for a single Magento backend to several HubSpot Portals. For example, if store A and store B both use the same Magento backend for order processing and inventory, and both have their own individual HubSpot portals, connecting both A and B with their respective HubSpot portals is possible. Despite connecting to the same Magento backend, the contacts and order data sent to HubSpot will still be segmented based on whether the order was placed on store A or store B.
If you are running extension version 1.1.13 or above, you can enable multi-store option in your connector settings on https://www.hubspotintegration.com. This would sync all the store data to your HubSpot portal. Keep in mind this goes against the best practices outlined above and EYEMAGINE may not provide the same level of support for this use case. You can still segment customers by website/store view in a single HubSpot portal using the "Store ID" property synced by the connector. The connector is also capable of syncing multiple Magento instances into one HubSpot portal.