You can find all e-mail templates in CMS Site manager -> Development -> E-mail templates. You specify site-specific templates by selecting a site in the dropdownlist in the mentioned location. You have to delete the global template first. Now just create a template with the same code name as the global one.
For example for the email “Order notification to customer” is always used the template with the code name Ecommerce.OrderNotificationToCustomer. So it means that you can create templates with this code name for each site.