Can anyone help me in figuring out what the cost would be to use the mult-channel order fulfillment from Amazon (as I understand it, Amazon will fulfill your order even if they come through your Shopify store directly and not through Amazon), but I am having trouble understanding what all of the associated costs would be from Amazon for that service?
You're right that Amazon will fulfill your Shopify orders through the multi-channel fulfillment (MCF) program. The costs vary based on your products, the customer's location, etc. But it's cheaper to fulfill orders placed on Shopify than those placed on Amazon because there's no referral fee. This article goes into more detail about how the MCF program works.
If you're looking for a way to automatically calculate your MCF fees for each unique order, you can use the FBA Shipping app. It allows you to pass those fees on to the customer in the form of shipping rates. You can also customize the shipping rates it shows. Hope that helps!