Hi @cas3,
I’ve also experienced the difference in order/line item values compared to credit card charges due to discounts, gift card balance, or points being applied to the order. The problem is that the Amazon export CSV does not include this information. Personally, I have been manually reconciling these orders and items by editing the item cost and order total to reflect the order details on Amazon. It is a pain, to be sure, but I am able to get an accurate reconciliation at least.
As for how to categorize the credit card transaction and avoid double-counting, I have a Transfer category for Amazon Purchase that I apply to both the credit card transaction and the [Amazon Order] transaction. Only the [Amazon Item] transactions have an Expense category assigned, so the expenses are properly reflected in my Savings Budget sheet.
I’m sorry I couldn’t give any better advice for reconciling discounts, but at least you’re not alone. 
I hope that helps!