Awesome, this is going to be really cool. I would drop the clip of the people on top to the clip with the train. You may need to drop the opacity to the clip of the people to make sure it is lined up where the people are. Use the mask tool to create a mask along the tracks and the people so it sits on the other clip. Then mark a key frame for the mask control points when the train is about to hit the people. The go a few frames ahead of the timeline where the train completely covers up the people. Create another control point keyframe and move the control points to line up with the train. You may need to tweak some of the in-between keyframes but that will create the appearance as if the train is running them over. Hope this helps.
Utah Video Productions
Check out my Motion Training DVD
Check out my Motion Tutorials