Hi Guys, OK after 1 Hour of figuring this out, this is how you export a movie from Motion with Alpha Channel included, so when imported into FCP it is a transparent file, ready to superimpose.
1) Open your motion project file.
2) Go to Export and choose the following preset settings:
Kind: Quicktime ( Click Options and choose Animation )
Export Preset: Lossless + Alpha Movie
Include: Video Only ( If thats what you need)
Click box if you want to render only play range
Click OK
Import into FCP, drag onto the top layer, and Voila it will be superimposed onto you under layers.
Thanks