In the template you can set the reference that needs to be set. You do have to define how to find the referenced object. So let's say you import salesQuotes. Then there needs to be an ID in the Excel line you are importing that can be used to retrieve the Customer. So if each row has a CustomerID that is available in the table Customer, this can be used to retrieve the parent and the reference can be set.
Hopes this helps,
Regards,
Ronald