Keep in mind any movement of the spaceship, AE camera, and/or green screen camera will throw off the perspective of your pilot and the shot won’t work. If it’s just one angle and the ship flies in a straight line, you may be able to make it work.
I’ve never added a pilot into a flying space craft, but this is how I would first attempt it. First, scale and position your pilot where he should go on top of the cockpit. Then create a group Null in Element and parent your pilot layer to that. Finally, draw masks on the pilot layer to make him appear inside the cockpit.