To save your email design as a template, click 'Save as Template' in the top-right corner of the designer.
Once saved, this template will become the active template. This means that next time you click on 'Save as Template' you will have the option to save as a new template or overwrite the existing template.
Note that if you leave the email designer and then come back, it will not be the active template. You will have to load the template again and then overwrite it.