Thank you for your question! It’s a really important one, so I’m glad you asked
You have 4 different shipping options in your store: free shipping, flat rate, flat per item and calculated.
When signing up we export all the shipping settings you set per item on eBay, so the default shipping setting in our stores is flat per item. But if you didn’t set shipping rates per item on eBay you can just choose the Calculated shipping option.