I\'m trying to use FFMPEG to create a video with one video overlayed on top another.
I have 2 MP4s. I need to make all BLACK pixels
You will not be able to get a "replace black pixels" approach to work properly. What you actually want is a foreground video with a real alpha channel that can be manipulated and tested before doing an overlay on a background. For an extended example that describes the problems, please take a look at my blog post on the subject. When using FFMPEG, an easy way to import alpha channel video is to use Quicktime with the Animation codec video at 32 BPP.