Make a color transparent!

This is probably a bit of a rookie request.
I am working on a video that includes some stuff from a graphic designer. He will be using flash to overlay some images and graphics etc, and exporting them for editing into my video.
If he chooses one block color that I need to replace with video, is there a tool that I can select that allows me to replace that color with video, like green screen? I haven't done any green screen work on Final Cut before. I will be able to corp some of his stuff as its straight edged, but there will be small animations with logos etc that need to be overlaid on to video. Can you help me? I am using Final Cut Pro 7.