For each order that is shipped via FBA, the customer notifications can be sent via 2 methods: 

1. Emails from Shopify (recommended option)

By default, Shopify sends order notification emails to the customers. Notifications are sent for new orders, order refunds, shipping confirmation, tracking updates, etc. More info Here

For each order shipped via FBA, the Connectr app updates order status on Shopify, and in return Shopify sends email notifications to the customers. 

2. Emails from Amazon

In cases when orders on Shopify are created via third-party apps, Shopify does not send email notifications. In this situation, the Connectr app can be configured to enable Amazon to send ship-complete notifications to your customers on your behalf. You can also choose to receive a copy of the notifications in your inbox.

To activate Emails from Amazon go to FBA > Settings > 'Emails for Amazon' line > check the customer / seller checkbox