You can achieve this in several ways, depending on the configuration of the module:

If you do NOT use the business policies: 

– If you want free shipping over a certain amount per item on the whole catalog, simply use a shipping mapping between Prestashop carriers <-> eBay shipping methods in which the amounts of the website carrier are free over a desired amount / weight- If you want free shipping over a certain amount for the entire eBay cart,
you can use the “Fixed Cost Domestic Shipping Rule ID” feature found in the Shipping tab of the module.
It allows you to determine a cost rule per additional item directly on eBay and have it applied for every item synchronized in the module.  To set the rule on eBay :
* Go to the ” https://www.ebay.com/ship/prf ” link.
* Click on “Fixed Rate Shipping Rule” and configure the rule according to your preferences.
* Take note of the rule ID under “Profile Name”.
* Go back to the module and enter the rule ID in the field “Rule ID for domestic flat rate shipping”.

– If you would like free shipping over a certain amount for a single item,
you can override the domestic shipping costs via the built-in editor on the product tab.

If you use business policies:
In this case you need to map, from the “Business Policies” tab of the module , shipping rules already created on eBay according to your needs.
This will make sure that the synchronization of products will use these rules, ignoring the other configurations in the module.