Multiple clips can be chained together to encode as one movie. Each clip is a chapter in the resulting QuickTime movie.

There is a switch at the bottom of the main window to create multiple movies or a single movie.  Moving the switch to the right-hand position will chain all of the clips together.

When creating a single movie, the format preset popup can be adjusted by the topmost clip only, and all subsequent clips will conform to the export properties of the topmost clip.