OK, I just checked the editor to make sure I'm using the right terms here. It's unfortunate that these different abilities have similar-sounding names.
Stealth Attack: This is an ability for regular combat units which lets them pick which enemy in a stack to attack. In the epic game, only submarines have this. The stealth fighter and bomber have this ability, but it does NOTHING for them because they do not attack, they bombard.
Stealth: This ability is for planes only and reduces the chance of them being intercepted by enemy planes and ground-based anti-aircraft weapons. Stealth bomber and stealth fighter have this ability.
Precision Bombing: Allows a plane to target city improvements only, rather than improvements, population, or units. I think the actual improvement targeted is selected randomly, but I haven't used this ability in a long time. Stealth fighter, stealth bomber, and F-16 have this.
Invisible: This unit cannot be seen, unless you move a unit onto the invisible unit's square, or your unit can "detect invisible". In the epic game only submarines are invisible. Submarines and destroyers have "detect invisible".
Hidden Nationality: The unit looks and behaves like a barbarian; it can attack and be attacked by anyone, even when war is not declared. Privateers have this.
As for the original question: to use the submarine's stealth attack ability, just attack a stack of enemy ships like normal. You'll be given a choice of which ship you want to attack. For the F-16, you have to use the precision bombing button instead of the usual bombing button.
I hardly even get to the Industrial age, never mind modern...
