The System Email Template is used when people sign up, request a password reset, and for any other system-triggered emails.
To edit it, go to the Settings > Your site settings > System Email Template option to the right of the page.
The content generated is identified by the [content] tag added on the editor. Your branded template may appear above or below the content.
Once you have edited your content, click save at the bottom right of the page. If you wish to see what it will look like when generated, send a test email by clicking the Send Test Email button at the top right corner of the page.