Continuing from a previous post: the GM rolls 3d6 on a dice map and interprets the results. You've already seen a list of suggestions, but the dice can show much more than those 25 results. If some of the dice match, or if a die lands on a boundary between two regions on the map, two values are interpreted together; the results can become very complex, such as Sea+Damned v. Living, which might be the crew attacking a helpless ship while sharks gnaw through the hull.
The lowest result on the 3 dice, in addition to indicating the threat, indicates the general strength of the threat -- how many hit points it has, relative to other threats. Many threats will only be 1 or 2, easily dealt with; rolling triple 6s will likely produce deadly, exotic threats.
To deal with the threat, the players will describe what actions they attempt. If you need to know the speed or effectiveness (strength) of their action, roll 2d6 and assign one value to each. If the character's action is opposed by another character,
NPC or PC, or even by a force, that opponent rolls 2d6 as well. The lowest speed result goes first; if the strength of the action is higher than the defensive strength, the action overcame the resistance. The GM may compare factors in favor or opposed to the action and adjust one side or the other by +1 or +2.
After the threat is dealt with, if the ship is heading for a specific port, one player and the GM each roll 2d6 and compare the highest result; if the player wins, do that much "damage" to the distance needed to be traveled. Some events, such as whirlpools and gales, may actually add to the distance; a gale, if the PCs are clever, might give a bonus to damage.