Currently, we support only Account level customization, ie, you won't be able to have unique email templates for sites if you have more than one site. However, we are planning to add this in the future.
Navigate to the Control panel if you are not there already by clicking on the Control Panel button in the top right corner.
Navigate to Branding -> Emails
Here you can customize 2 emails,
Invoice Email: Invoice sent to Guests after each successful purchase
Account Email : An Email containing info about how to add more guests etc
Invoice Email
Use this option to edit the Invoice email send to Guests
Account Email