If you import the motion file directly into your Final Cut Pro timeline you maintain all of the Alpha Information. If you want to export a video I find this to be the easiest:
File, Export. Click on Options… Change compressor to Animation. Click on the Advanced button. Make sure it is set to Millions of Colors +. The plus is the alpha channel.
Utah Video Productions
Check out the Graphics Demo Reel I did.
Check out my Motion Tutorials