You can create new system email templates and modify existing ones from Setup > Company > Email > System Email Templates. The process for creating and modifying system email templates for web store email is the same as that for creating and modifying other types of system email templates. For more information see:
It is important to remember, that when you create a new system email template for a web store email, you must attach it to one or more of the following template categories:
Web Site Order Notifications
Web Site Digital Delivery Notifications
Web Site Other Notifications
For more information about template categories, see the help topic System-Automated Template Categories.