Amazon orders that are also fulfilled by Amazon are part of the Amazon Fulfillment Network (AFN), which means they shouldn't be fulfilled using any third-party system -- including ShipStation.
For search visibility and reporting purposes, you can configure ShipStation to import those orders into the Pending Fulfillment or Shipped statuses.
Note: Orders imported this way will count toward your ShipStation subscription plan's shipment limit.
To enable this option....
Go to your Account Settings (the wrench icon in the upper right).
Next, select Selling Channels and then Store Setup from the sidebar on the left.
From here, click Edit for the Amazon store that needs the AFN orders to import for visibility and reporting purposes.
Under the Store Information sub-tab, scroll to the Store Settings section and check the box for the Import FBA Orders.
Don't forget to Save Changes when you're done!
*Note: This option is currently only available for US-based Amazon.com accounts.