Yes, it is recommended that you only allow for one order confirmation email to be sent upon placement of a multiple shipping address order.

To get this set up, follow these steps.

From your home Shopify dashboard, go to Apps –> Giftship –> Ship to Multiple Addresses –> Order Processing. 

From here, choose to disable notifications for follow up orders.

We recommend implementing the best practices found in the following article, which outlines how to edit your Order Confirmation email template to account for multiple shipping address orders:

Gist Support