I did know that you could pick up bodies and move them around, but never really saw a reason to do it. Earlier in the game, when I was sneaking around the mansion, I would pick up bodies just in case to throw them out of view of other guards or the cameras. For that ship level, I just never though that tossing the bodies would let me still sneak around.

Still, I'll stick to my previous response of just shooting everyone.

How do I get to the control room in the train station? I crawled through a hole in a wall. There are two guards. I can sneak past the first guard by crouching/moving past him. The 2nd guard at the door always sees me and shoots me. How do I get past the 2nd guard?

Wail until the 2nd guard walks through the door and then kill the first guard. Then walk through the door and the 2nd guard will be standing there looking at the billboard, take him out with the knife and move on through the next door.