Custom emails can be used in 2 different ways. One reason to be sending a custom email could be to notify a customer their order has been dispatched. Another reason could be to tell the customer that there is a delay in their order process or that you have refunded an item off of their order. See footer of this article for further information.
The first thing you will need to do is set you custom email up. To do this you will need to go to your settings in the back office and select the tab 'Emails'. You will then arrive on the page shown below where you will need to select the 'Add Custom Email' tab.
You will then go to a page where you can set up your email title and its content as shown below. Remember to make use of the custom tags for the customers name or company contact details and simply click 'Update Email' to save your changes.