Kain- offensive, same ship as Rydia (I assume this will be one of the battleships). He's a strong fighter, and he's got his jump skills, so if there's a time/place where someone leaping high into the air is of use, he's your man.

Mulder- defensive, so on the main ship. He's got guns and FBI skills... and general Mulder-y skills. He will probably be happy to blab on about any mythology he happens to know about sea monsters and the like. Though he himself isn't exactly the most comfortable on boats!

Vincent- offensive, and my preference is for him just to be on whichever ship Kain isn't on. He fights with a gun, a claw, and four demonic entities inside him. He could make a good scout- former Turk + enhanced weird physiology- so I'll throw him there!