How do submarines display navigational lights when afloat?

The primary underway lights are the Port/Starboard running lights, the rudder light, and a flashing yellow dome light.

On older boats the Port/Starboard lights were housed in the sail, and had to be deployed manually by an Electrician's Mate once surfaced and the bridge manned. Today they're likely deployed automatically. The Port light is Red, Starboard is Green.

The rudder light is on top of the rudder, and is an electrically powered white light.

The yellow flashing light is deployed via a raisable mast; it is a navigational indicator to all ships in the area that there is a surfaced submarine underway. The light is used because submarines are very low in the water, and are difficult to see in good conditions with standard running lights. Without the yellow light, it's easy to mistake it for a regular sailing or fishing vessel.