Its a Perception check. The DC starts a -10 to hear a battle. Being below decks raises that by 5 (through a door) or 10 (through 1 foot wall), depending on how thick the deck is, and being asleep raises the DC by 10. So its a DC 5 or DC 10 check, modified by the distance the battle is away from the party (+1 DC per 10ft distance).
Edit: I assumed the PC on watch was above deck, with the rest being below decks. If the watcher is just sitting there in the same room with the party, there is no penalty for distance, or hearing it through a door/wall/floor. The DC would only be -10, +10 for the party being asleep. So DC 0 Perception check.
And even if the party gets unlucky and fails a check, they can just make another check the next round.
I would say "do you want them to wake up or not?"
In RL, they wouldn't hear a thing, and even if they did they probably wouldn't wake up. However, it is a gaming-trope that you get a chance to wake up when combat kicks off near where you're sleeping. This then allows players to go join the melee wearing their pyjamas which is fun for the ref to finally get a proper chance at the party tank.
You'd be perfectly justified to set the DC of the perception check too high for there to be a realistic chance of anyone making it (all those decks, distance, closed doors). Do this if it's important to the plot that they not wake up, but be prepared for the party elf to point out that he's not actually sleeping and has a bonus on his perception rolls as well. If you're intending it to be an interesting fight that the players win I'd say set a DC that will be hard (say, DC 20) but allow them to roll every round at a gradually decreasing DC (say -1 per round, or -2 if their ally is shouting his head off, and another -1 for every new combatant). Then the poor guy on watch can fight defensively, run around on the deck trying not to get cornered, climb the rigging yelling for help and try to hold out long enough for the rest of the party to join in. (And hope that they don't insist on putting hteir plate armour on before they leave their cabin).
Yar!
This is all covered by the Perception skill.
Jeraa summed it up fairly nicely (but I have some additional considerations).
Base:
Hear the sound of battle: DC –10
Modifiers:
Distance to the source, object, or creature: +1/10 feet
Through a closed door: +5
Through a wall: +10/foot of thickness
Unfavorable conditions*: +2
Creature making the check is asleep +10
* I included this as well, as the sound of the ocean/waves creates a white-noise to a sleeping person who has become accustomed to it, as has the constant creaking and shifting of the ship itself.
Why?
Comparing to other base DCs, we see that:
Hear the details of a conversation: DC 0
Hear the sound of a creature walking: DC 10
Some people don't make a lot of noise when they fight (even when not actively using stealth), and a solo fight or even a small group fight doesn't make as much noise as large scale battle by the very nature of the event. Of course, if the PC up above starts screaming for help while he fights, that's a whole different story, bringing the base easily back down to -10 (modified by circumstances as listed in the skill entry) and new perception checks by those sleeping below.
~P
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Because most people standing watch elect to "sound the alarm," I would easily rule this a DC 5 Perception check (-10 from sleeping, +10 for the sound of someone yelling in battle, +5 for terrible conditions). I'd lower this to 0 IF the attack happened somewhere close by. If the PCs are sleeping further away (than below deck), I might increase it to 10 or 15. Really, it all depends.
That said, I also use Passive Perception (characters are assumed to be "taking a 10" unless they are actively searching for something) in my games. So, in most instances, I just pass a note to the players (or wake the whole group) and describe the situation.
Once they are awake, I require a move action to get up, require they don armor as normal (which, for heavily armored opponents, can take a bit of time), and then respond.