After you create a customized e-mail template, be sure to configure your account to use it when applicable. There are four ways to assign an email template to an order:
1. Apply the email template to a specific store.
Head to your Account Settings (the gear icon in the upper right).
Next, select Selling Channels and then Store Setup from the sidebar on the left. 
Click Edit for the store you'd like to assign this email template to, and then the Notifications sub-tab. Adjust the "Shipment Confirmation Email" and "Delivery Notification Email" options as needed.
Then, Save Changes at the bottom of the page.
2. Trigger a specific email template for orders that fit certain criteria via automation rules at the Account Settings gear > Automation > Automation Rules. For example, assign a Shipment Notification email template that includes a coupon code valid on your online store for orders above $300.
3. Override the default email applied on a single order by navigating to the Orders tab, click the applicable order number, and change the template in the "Order Templates" section of the details screen.
4. Apply it to selected orders or all orders in a view using Bulk Actions, by going to Other Actions > Apply Bulk Action.
*Please note that any changes to the Store Settings or Automation Rules will only take effect for future orders.