I am bringing in a lower 3rd clip I made in motion to final cut 5. In motion, everything outside of the lower 3rd is transparent, when I input it into final cut, the transparent portion comes up black.

any thoughts on what I am doing wrong?

are you exporting/rendering the clip out of motion? if you are export with the animation codec in millions of colors + which is the alpha channel but you can also just import the motion project file into final cut and it will have the transparency and if you want to make any changes just right click the file and choose open in editor, make your changes save in motion and "poof" it updates in final cut.

yes, rendering it out because we are using it in final cut 5 and 4.5 projects.
in the quicktime output, it is set for color+alpha.

figured it out

set to lossless + alpha in the save dialog box