The Preferences window is where you configure the breaks and other options.
At the top of the window there are four buttons:
Pause: If you expect to be busy and don't want to be disturbed for breaks for a while, you can pause Time Out for a specified time interval. It'll automatically resume breaks after that time. You can also pause indefinitely, i.e. until you manually resume. When paused, this button changes to resume, so you can resume at any time.
Help: The help menu includes commands to show the standard About window, show this help, and show various related web pages.
The window also includes a sidebar that lists all of the breaks in priority order; you can drag them to re-order, with the most important break at the top. Less important breaks can be automatically skipped if they are too close to a higher priority one; this is an option on the Break Schedule page.
For each of the breaks in the sidebar, a color label and name is displayed. These can be edited on the Break Name page. The item also displays when the break is next due, and last done. These can be displayed as relative times like "15 min, 23 sec" or absolute dates with the calendar date and time; see General Options to set this.
When hovering the pointer over a break row, two buttons will appear: Start and Options. The Start button will manually start the associated break, so you can see what happens, or to force a break now. The Options button will show a menu with additional commands, including the ability to defer the break, disable it so it isn't used, or delete it entirely.