The Orientation can be set to Vertical (Portrait) or Horizontal (Landscape) either from the Documents tab or from the Cutter menu.
In the example below, we have the Mat Size set to 12" x 24"
with the Orientation set to Vertical (Portrait)
Below is how as 12"x24" set to Vertical (Portrait) would be relative to the cutting machine.
Below is the same 12"x24" mat size but with the Orientation set to Horizontal (Landscape). Please note the mat size is still 12"x24" and not 24"x12". Even though visually on the screen it would look like it is 24"x12", the actual mat size is still 12"x24" but just rotated to be shown as Landscape.
Below is how it would be relative to the cutting machine.
This is cutting idential to the previous Vertical (Portrait) example. It is just the view is rotated to Landscape here.