You can create new email templates and modify existing ones from Setup > Company > Email > System Email Templates. The process for creating and modifying email templates for website email is the same as that for creating and modifying other types of email templates. For more information see:
It is important to remember, that when you create a new email template for a website 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.