I am looking to super impose some footage on to a rather shakey handheld footage that I have been given. The top layer will always be in the same place in relation to the bottom layer but there must be an easier way to do this than keyframing every frame to fit it in. Essentially trying to superimpose some footage onto a shot of a screen, but the screen keeps moving.
This is called motion tracking. You can use Mocha, which is a planar tracker that comes with AE (tracks planes) or AE's corner pin tracker. There are tons of resources on the web for this. The best technique depends on the shot. There have been recent questions about this on this forum.