You can specify the templates to be used on SYS:Notification Messages Form.
So if the notification are OOTB you can go in and set the HTML template Name on the entries.
If its custom notifications without using the SYS:Notification messages , you can set the template to be used on the Notify action itself.
You will need to add the HTML templates to the Email Templates form first.
Hope this helps. If unsure please provide more details of what you are trying to achieve and notification type.