Sorry to side step the main question, but if you are writing a story about buccaneers, you've set the book in the wrong period if you want to be historically correct. If you just want pirates - as in men who took vessels all vessels regardless of country - you'll want 1714-1724 (though you could also do 1700-1713, though activity was down). If you want the guys who raided the Indian Ocean of rich prizes from India (such as Mogul vessels), 1690-1700 (or 1720-1724) will do you. Raiders of Spanish possessions and ships in the South Seas/west coast of the Americas, go 1678-1690. Then, your proper buccaneers who raided mostly the Spanish (with many raids on land targets) - that could be 1630-1680 at the broadest, though the 1660s work out really nice for that since at that point the Buccaneers have Jamaica to use as a place to operate out of.

1763 - not the age of Piracy by any means, especially not buccaneers. I want to say this is discussed in Part 1 of the podcast I did on piracy with /u/eternalkerri, but it might be part 2. Click for the the discussion thread for that podcast so you can access it. I don't know how familiar you are with pirate history, but in that discussion thread for the podcast, I have lists of book (in particular the one that is linked concerning the "9 Broad Topic books") on there that might be a big help if you have little or no familiarity.

As for the stowaways - honestly, reading academic works on maritime history of the era, it's not a topic that's really addressed in any note. As far as I know, there is no particular weakness and hiding place specifically vulnerable to stowaways. Getting on the ship, as far as I can see, is a matter of timing, as in "make sure no one is looking." Once on the vessel, finding a place that isn't frequented much (which can be difficult) so as to make it easier to hide (or at least be able to disguise your presence really well). It doesn't help that ships all have many differences from one another, so it's hard to make a rule of "this is the best place to hide a person". Also, there is the chance that someone (or several people) are helping the stowaway hide, which is a big help. The one worry I would have is not stowing away anywhere near the bilges. Sure, few will come down there unless absolutely necessary, but there's a reason for that - over time the build up from human waste, sea water, and other filth in the ship gathers and creates such a horrible smell and gases that it's been known to kill people.

That's all I can really offer. I see that this post didn't get upvoted (in fact, it's at zero right now), you might want to leave off that this is for a fiction novel about buccaneers - I think it had the affect of making people not taking this question seriously (and maybe posting at a better time - I'm not sure that 4:00 AM EST early Monday morning is that great a time for a question - timing is everything with internet postings). It's sad to say, but a lot of people are tired of people basically coming in here and having fiction writers come up with questions that practically end up with the people answering doing the writing/research for the fiction writer. Granted, your question is not part of the bad questions I've seen posted in that way, but people still see that stigma attached.

Good luck on your work.