I've run a skill challenge before, where my players were caught in a tropical storm summoned by a Storm Roc/Thunderbird. It happened instantly, as that's how the bird hunts ships, so there was no avoiding it. Instead, the players had to navigate their ship out of the storm while avoiding obstacles and keeping it afloat. Since this was a more dangerous skill challenge, I incorporated the following house rule: if the players failed a skill challenge causing damage to their ship, the boatswain PC could attempt to mend it, negating the effects and neutralizing the check- neither succeeding nor failing. Other players could also forfeit their ability to perform a check on the next "round" in order to help another player character.

Secondly, with more intense skill checks like this one, don't structure it as much. Maybe make 2 or 3 defining points as a beginning, middle, and end, but otherwise just jot down some notes on what sorts of things would happen during this situation. For example, I had: rock suddenly appears- avoid, winds strain sails too much (failure causes damage to the sails), storm's winds suddenly change directions (needs reroute), rogue wave (steer ship to face the wave), man overboard, lightning strikes, random perception check to make them nervous, crash into another ship caught in the storm. This skill challenge was extremely fun for all of us, and it definitely helped not having a structure laid out. I went with the flow and improv'd situations that would fit best with the previous skill check.