The better your boat rules are, the better your campaign is going to be.
Unfortunately, I've never seen rules for boats that are what I would consider excellent, especially when you get up to non-traditional 'Great Age of Sail' style ships.
Some important points:
1) There are skills around handling boats and navigation that are important to a game that occurs about boats and ships.
2) Ships have damage resistance, and the bigger the boat the higher its damage resistance. A ship with the general build of a 72 gun ship of the line has hardness/damage resistance of around 18.
3) As a result of that, realistically, ships of that size are virtually immune to torsion engines like ballista. But you may want to ignore that and have torsion engines roughly as effective as cannon because the side effects of gunpowder in a campaign world (ei, readily available explosives) are significant and tend to promote a non-heroic world.
4) If sailing ships exist in a magical world, then there is by definition a thriving economy around protecting those ships from magic. And in particular, no large and valuable ships can really exist in a world where fireball is a low level ability (and hence common and economical), unless equally common and economical ways of defending objects from fireball exist. In other words, magically protected sailcloth has to be cheaper than a wand of fireballs, and any world where fireball casting mages occur in uncountable numbers (ei, you can't list every 5th+ level wizard in the game world) also has large numbers of similar level hedge wizards producing low cost magical goods for the non-adventuring economy.
5) The sailing characteristics of vessels - how fast they can move both tactically and strategically, at what points to the wind, how much they can carry, how large of crew they need to be minimally functional, how they respond to weather, what can cause a ship to capsize, what happens if they impact something, how crew you need to deal with leaks, how quickly can things be repaired, how much damage can be repaired at sea, and what facilities are required to complete repairs, how magic impacts repairs, how spells effect ships, how a crew's quality impacts performance, how long it takes to build a ship starting from raw materials, how much a ship costs to buy, different quality levels of a ship, and on and on and on are all things you're going to find out you need. Much of that you'll need on day one, and most of it you'll need before say session 30.
I've been involved in seafaring campaigns before, and the first thing you notice whenever you use published seafaring/ship rules is that THEY ARE NEVER PLAYTESTED EVEN BY THE PERSON WHO WROTE THEM. I put that in all caps because not once have I ever tried to use a set of rules where it didn't turn out to be true. No matter how good looking the rules are, once you try to put them in practice, you'll immediately run into huge problems and have a ton of questions the rules don't answer or a ton of balance issues the rules apparently overlooked. You can deal with that either by using lots of hand waving, with the result of having players being asked to play a sandbox campaign where they lack even basic control of the most important aspect of the campaign, or you can hammer out your own rules using what you have as a framework.
I'll give you a very basic example. Pick up any set of rules supposedly covering sea faring in D&D, and ask a very basic question of it, like, "If I erect a Wall of Fire spell on the deck of the ship, is it fixed relative to the deck of the ship, or in absolute space relative to the point I cast it at so that the ship then sails out from under it? Is the same thing true of a wall of stone or a wall of iron?" If it doesn't address questions like that explicitly, the rules have never been play tested. More comically, if all damaged ships eventually sink (something actually encountered in one set of rules I actually tried to use) regardless of what the crew does, you can guarantee the rules have never been play tested.
