You can have only 1 global template, but you can have as many custom HTML templates as you wish.
When we are sending the mail we are trying to find out if you have a template that matches all criteria - class name and function name. If we find such a template we are going to use it. If we don't, then we will use the global template - if one is provided. If you don't have a global template, then we will send the mail as plain text.