Have you tried laying the .motn file in your FCP timeline and then rendering? As long as your motion project and FCP timeline have the same settings it should result in the highest quality.
Are you editing SD or HD uncompressed? If it is SD for broadcast…create your graphics at 720×486. If they are HD 720p create them at 1280×720 and if HD1080 create them at 1920×1080. Photoshop has all the presets when you create a comp.