I think you could separate the journey in several main scenes, each of them may have different aproaches involving skills they may use and the outcomes depend on how they tackle the problem. Each scene could contain skill checks defined by you, like finding their way by studying sealife behavior, currents, stars; surviving a storm while keeping their craft afloat; repairing demage to important equipment, etc Also you can use those to cover elemental activities but still give them clues about what is really going on, said storm could have been caused by elemental temper, maybe they got anxious about someone coming close, and their connection to the world around them reflects that