When you click on the new notification button in the toolbar, you will be presented with this window. It contains a dropdown of all of the currently available notifications, as well as a master notification.
A master notification is used as a template for any notifications created after it. When you create a new theme, a master notification will automatically be created for you. If you know your theme is going to look basically the same for all notifications, you can create a master notification that already has a background image set, contains some text, and any other items you want.
You can add as many notifications of as many types as you want. When an event happens, Guifications looks at all the loaded themes, checks how notifications of that type that they have, and chooses one at random to display. This gives another level to customization, since you do not have to create another theme if you want to make the same notifications have subtle differences.