The submarine is located on the right side of the board. Shooting the ball into the submarine earns 3,000 points. Sometimes the ball shoots back out of the submarine and sometimes it shoots out from under the boat after going in the submarine. This seems to be random, not related to the lights.
There are lights on either side of the submarine entrance. You get about 1,500 points for lighting each one. You get 3,000 points for entering the sub with both lights lit. Sometimes you will light one of the lights on the way into the submarine so you might receive 4,500 points.