First off, on the subject on aiming, wich has come up:
There were calculations for range and aim used in the artillery during the black powder era that was quite accurate. More interesting, a veteran artillery crew mostly made the aiming on gut feeling, and was surprisingly accurate, despite using very crude methods of aiming, such as using wedges and woodparts to increase/decrease elevation.
Therefore, for me aiming seems better left to the gunners, with either some sort of penalty for a rookie crew, or a bonus for a veteran/crack crew.
Then on to subject:
As stated earlier, being shot in the bow should become raking, wich would then make a certain type of damage to certain specifics, as the crew, rigging or so, this because the bow of a ship is very narrow, and a very bad angle to sink a ship from, why this mostly resulted in just raking shots.
Being fired upon in the stern could potentially be dangerous for the ship integrity, since this area, while narrower than the broadside, still is plain, and not pointed against the firing ship such as the bow, This could differ depending on the ship, since this is more valid on bigger ships, while on smaller ships this as well more turns into raking shots.
Other than that, all I might suggest is some sort of morale value for the crew. If morale stays up (and better crews could have better morale etc), the crew (or main part of it) continue to fight, while morale breaking (due to morale penalty from ship sinking) would make the crew stop fighting and either strike their colors, or abandon ship,