If you're shipping through Amazon's Seller Central to obtain "Prime" status, you'll need to configure Finale to properly decrement the inventory.
In your Integration screen, click edit configuration next to the Pull Sales to Finale line in the Amazon connection (See below).
Choose Automatic to run the task continuously.
Choose the location you want the orders to decrement inventory from.
(optional) Assign the customer to Amazon FBM Prime.
Note: customer must be created first.
How do I manage my FBA orders via the ShipStation integration?
How do I use the reorder function to maintain FBA stock levels?