Undead Crew.

[MiuKujo]

I announced to my party last week that we'd be starting our new campaign in an archipelago and to plan 3rd level characters accordingly. There was only one whom chose something actually interesting that I'm not 100% sure how to handle. They decided to go full evil and he wanted to be a Dread Necromancer(Heroes of Horror). His goal is to make a ship crewed by the damned. A literal skeleton crew. They work for free. They never tire. And with his broke ass Charisma score (32 point buy) he can have something on the walk of 14HD of undead per level under his command.
Therefore my question is, could the skeletons of sailors proficiently sail a ship under an un-experienced leadership. (None of the Party actually know anything about sailing) They figure they could go full subterfuge and get their way into large ships (men lost at sea, dock hands looking for work, etc) then use a few low end area spells with stuff like the Fell Animate Metamagic feat in order to wipe out whole crews as your average human has ~5HP without class levels. There might be the odd one that has class levels, but nothing 30+ skeletons couldn't kill.
I'm not looking to restrict them or make it stupidly difficult to pull off. The thought of a literal Black Pearl going around taking out other ships in piracy is pretty awesome. But I don't want to make it unbalanced either. How much does an undead retain of its old life after it's removed. And what happens if you res a 5th level character as an undead. Does it retain class and skill ****? Documentation on undead armies seem to be pretty few and far between so I look to your combined archival knowledge of all the goodies to lend me assistance.

[Thrice Dead Cat]

Bog standard skeletons have Int -, making them mindless and unable to retain any skills they may have had in life. However, if he uses a different template that leaves the corpse with an Int score, then he could be in luck. It would then depend on if the new undead retains knowledge from its life or is more of a blank slate.

[DrMotives]

Animate Dead won't do, those skeletons can't do anything as complex as sailing without constant micromanagement by the necromancer. You need something with a mind, like the Dread Warrior or Bone Creature template. For non-template undead, something smarter like ghouls or wights can work. Basically, something smart enough to take at least a rank in Profession (sailor), and of course it needs to be corporeal.

[Necroticplague]

Try introducing him to Haunt Shift. Lets you turn undead into haunting presences that can control objects. So instead of a literal skeleton crew, you have a ghost ship that runs itself.

Default skeletons lose all skills as a result of being mindless. They can make anything that's DC10 or less, so sailing the ship under normal conditions should be fine, but you're in trouble if things get even a bit rough. So Animate Dead is out. Create Undead, however, can make Bone Creatures, which look like skeletons, but are still intelligent, and have all their skills from life.

[Segev]

If you want to allow him to do it, I would suggest allowing him to research a custom spell that enchants skeletons under his command with a purpose-build job/set of skills. Essentially giving them Profession(Sailor) at a certain bonus which can be used for any task related to sailing the ship.

[BowStreetRunner]

Unfortunately, Awaken Undead is going to be out of reach for a 3rd level party for a little while. Undead Leadership is still a few levels away as well. You might advise the player to focus on acquiring a crew of normal sailors for now, supplementing them in battle with undead, until the character starts to gain the ability to crew the vessel more fully with undead sailors.

[Necroticplague]

If they use Fell Drain instead of Fell Animate, they can get wights, which are intelligent enough to sail. Since Aid Other is DC10, skeletons can do that. So Wights with a few Skeletons helpers Aiding them could also work. Alternatively, they can make the Profession (Sailor) checks themselves, have the skeletons Aid Other, and fluff it as the skeletons doing the task (with your check result indicating how closely you were able to give them the exact orders they need).

[John Longarrow]

Course for a long term goal, you could suggest they try their hand at whaling. Catch one good size whale, gut it, outfit the inside as a cabin, then animate and awaken it. Poof, instant intelligent submarine!

[Fouredged Sword]

Skeletons CAN act as crew, they just need management from something smart calling orders. They will never be good at profession (sailor). You want undead who can think. Animate Dread Warrior can do this. They take a sharp Int penalty (-6) but nothing hurts their Wis, so all you need is a skilled sailor who you murder and animate into a first mate. You will likely have to purchase a scroll for the spell as it is 6th level, and it's expensive, but you only need the one to make the skill checks.

Find someone with decent wis and ranks in knowledge (geography) and Prof (sailor). I would put a preference for rogues, so try a pirate.

Another interesting option is to make a necropolitan and then control him with rebuke. This is likely cheaper, but the creature loses a HD and you have to take them alive to make the transformation. They also are likely to betray you if you don't maintain the rebuke. You are also restricted to half your HD worth of creature.

As for his crew, I would suggest Sahuagin, as they are 2HD creatures with good stats and a natural swim speed that nobody will mind if you wipe out a village or two. A few advanced Sahuagin make good brutes. The 6HD versions are large.

Note, the blood frenzy ability is not con based and improves their natural attacks, so they maintain it despite being skeletons.

[Inevitability]

If they use Fell Drain instead of Fell Animate, they can get wights, which are intelligent enough to sail. Since Aid Other is DC10, skeletons can do that. So Wights with a few Skeletons helpers Aiding them could also work. Alternatively, they can make the Profession (Sailor) checks themselves, have the skeletons Aid Other, and fluff it as the skeletons doing the task (with your check result indicating how closely you were able to give them the exact orders they need).

Problem: the wights created by Fell Drain are in no way under your command. Rebuking them isn't guaranteed to work, and you don't want a wight attacking you as a 3rd-level party, no matter what challenge ratings might suggest.

[Segev]

If you're okay with Pathfinder spells, there's this one, called, appropriately enough, "skeleton crew (http://www.d20pfsrd.com/magic/all-spells/s/skeleton-crew)."