In the upper menu, go to the Notifications tab, then click on the Activate New Notification button found here.
There are two main notification types based on destination: Admin and Student notifications. You can also decide if a notification affects all of the courses or just a specific one.
When typing your subject and message, make sure to use the shortcodes found on the right hand side of the page.
Additional settings can be found by navigating to the General Options -> Notifications tab.
You can also activate the option for Pushover Notifications by going to the Magic Feature tab and setting this feature up. Afterwards when creating or editing a notification a new section called Pushover Notifications will appear.