Based on your settings, that is the right way for video (export to 4444 codec) What's not working? Is it because you see the black background when it opens in Quicktime? What happens when you bring this back into Motion or another video app, is the black background area transparent?
FWIW, you will not get the same result with video that you would with a still frame in say Photoshop where a layer may be transparent in the export and you don't see any BG color in preview or a web browser. Video will always have some sort of a BG color that things are premultiplied against that gets masked out when layered with other elements. Apps like Quicktime don't do anything to show the masking , but once you bring movies into apps like FCP, Motion, etc. the transparency of the movie should work.