Our system does not support multiple eBay stores from one ecommerce store.
At present, we support 1 ecommerce store, 1 account in our system (eBay LINK/Omnivore) and 1 eBay store on eBay.
If you connect 1 eBay store to multiple ecommerce stores using our platform you will have a number of listing and order failures.
Please put in a feature request if this is something that you would like.