Have no fear of history, my lads for you see, we already thought about that, we did...
Strange things happen out on the edges of the world because the greater bulk of disbelieving humanity is back in Europe. There really are sea serpents and worse prowing the waters of the western Atlantic. Islands shift and change shape till enough cartographers fix them in place. Sailors superstitions are more than mere fancy.
In short, Skull & Bones, for all the extensive historical research we did, is meant to be fun. It was designed so that a purist could run a historical game with little modification, but the underlying presumption was that most of you would rather run a swashbuckling game with supernatural and horror elements occasionally tossed in.
Remember that just because you start a game under "correct" historical terms, doesn't mean it has to stay that way. For those of you with history buff players, I'd suggest chatting with them about the year you intend to set your game - the Skull & Bones' default is the "Golden Era of Piracy" which is roughly 1690 to 1725, give or take on both sides. Big events in Europe take awhile to get to the Caribbean anyway, though the War of the Spanish Succession (1701-1714) and its eventual ending effect piracy in the New World drastically. Once you've established the year, you can decide any big events that are going to happen on your own and pass along to the history buffs that all else is subject to change...
I did a lot of testing of the mechanics with the bokor and the hougan so they would remain balanced, yet "feel" right for the setting. I talked to a bunch of west coast players, at cons, stores and what not. The introductory adventure I ran at a couple of cons called "Welcome to the Account" is in the book. One of my big concerns was how players would react to the almost wholesale stripping of common magic items. It went over pretty well, actually, most stated something I was already thinking: If you're going to get rid of most magic items, make the ones that are still around cool and unique. While access to "small" magic items, e.g. trinkets that give a +1 bonus to this or that, are relatively common, most of the magic items that we typically associated with d20 are non-existent. However, the few that are around are very powerful / lesser artifacts. Most of them have a price. In fact, that is a theme throughout Skull & Bones - mystic power always has a price.
The game I ran involved the doings of a Sea Dog captain and his crew as they struggled against the nefarious influence of a sea-born cult called the Brotherhood of the Shark. The Shark brethren carried barbed awl hooks and some of them had teeth that had been filed to razor sharpness. In fact, many of them had the "Bottom's Look" to them. The Bottoms is a small community on the Dutch-controlled Caribbean isle of Saba. Think "Innsmouth Look".

There was a lot of sinister doings in my game, at one point the players ended up sacrificing a cabin boy to appease a sea monster, that sort of thing.
Afterwards, my players all said they'd had a blast, but several of them told me I'd given them nightmares, which sounded like I did my job right. Skull & Bones isn't as grim as I am.
Joshua - You were destined to buy it anyway. Your sig line "Alea Iacta Est" is Adamant Entertainment's motto.
