If the General Preferences option to display the status in the menu bar is enabled, Time Out includes an item in the right-hand-side of the menu bar.
See the General Preferences for more information about customizing the appearance of the menu bar item.
As discussed there, when the Dock icon is shown, clicking the status item will toggle the Preferences window. But when the Dock icon is hidden, clicking the status item will instead display a popover from the status icon.
The status popover is basically the same as the sidebar of the Preferences window, with the buttons along the top, and the list of breaks and options. Choosing one of the breaks or options will expand the popover to the full window with an animation (which can be disabled via the Advanced Preferences if you wish).