Ship with Amazon can be configured to work in either of the two modes:
For each FBA eligible order on Shopify, you need to manually confirm FBA shipment by clicking the 'Ship with FBA' button. Only after the confirmation, your order will be sent to and fulfilled by Amazon FBA.
The orders on Shopify will automatically be sent to and fulfilled by Amazon FBA without manual confirmation. The shipping status will be available on the app dashboard. You can subscribe to email notifications for each FBA order.