Sold our first order on Amazon and the customer chose Expedited Shipping. On Shopify we have Free shipping + customer can pay. The item in question for USPS Priority shipping is about $30 our cost. But the Amazon customer only paid $8.99 for the Expedited shipping. I have confirmed on Shopify the shipping rates we've been sending out orders with no issues. On Amazon the only thing I see in the shipping for the item is "Migrated Template" so I am not seeing a way to make sure the customer is paying the correct shipment amount if they choose something other than free. What am i doing wrong?
Are you using Shopify's built-in Amazon fulfillment integration? If so, you'll have a hard time matching Amazon's shipping rates. Shopify requires you to set up flat rates for that integration. And it would be nearly impossible to create shipping rates that would cover every possible combination of products and every customer address.
If you want to automatically pull in Amazon's real-time, dynamic rates, you'll need an app like FBA Shipping.