We are looking to test the waters with FBA for one of our smaller products. Below are a few points on how we currently operate.
We are looking to continue to fulfill non-Amazon orders at our DC (at this point). We don't have the sales volume yet to justify moving all inventory to Amazon FBA, and we still need to fulfill orders from our other sales channels.
1. You can set the Amazon fulfilled SKU's at the product level, and they'll be assigned to Amazon fulfillment service when the order is placed.
2. You'll switch the "inventory managed by" setting to Amazon Marketplace Web.
This is the most common setup I see with people using our app Order Automator, the app automates amazon fulfillment so when line items in the order are assigned amazon fulfillment service, the app automatically requests the fulfillment to Shopify.
For a deeper guide, options, explanations about fulfilling with amazon and automating fulfillment: https://speedboostr.com/automate-order-fulfillment-on-shopify.