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Both Layer and ColorKeyMask expect a clip as their parameter, and not an avs script, so you should have it ALL in one script, and you should start it with for example
GOUT = mpeg2source("path_to_GOUT_clip.d2v")
SE = mpeg2source("path_to_SE_clip.d2v")
GOUT = GOUT.Trim(..., ...) #the start and end frames if you want to do it only with one scene
SE = SE.Trim(... , ...) #the same
GOUT = Crop(... , ... , ... , ...).Lanczos4Resize(720, ...) # crop it and resize, the numbers are depending on the format you're using (NTSC / PAL)
#and later use
Layer(GOUT, ColorKeyMask(SE, $000000, 10), "add", 255, 0, 0)
That's one method. If you don't wanna do it this way, tellan wrote a couple of month ago a different method on chroma keying in his "Lancer project" thread. Maybe it's worth reading.