Make sure you kill everyone on board and set the bomb. Go set the other bomb, run back to the control room, kill the guy there, climb the ladder and get off the boat. Once you are off the boat then worry about the other guys.
**Practicing the dark art of turn signal usage since 1976.**
Kill all the axis around the sub before entering it. You will have less of them shooting at you when you leave. also have your sniper rifle ready before exiting the sub.
What part are you stuck on? kill everyone in the sub before you plant the bomb, then get out of the hatch and shoot everyone in sight while you run towards the crates in the rear. I stayed at the crates until i sniped and killed enough so where i can run out of there safely.