I prepped a spreadsheet with each suspect, their motive, how they did it, and how they spent the night if innocent. I don't recall there being much in the way of physical evidence or ironclad proof of guilt. IIRC, it's more about the various NPC's testimony.
Since the scenario is designed to allow for several different murderers, many on the crew have really plausible motives. The crew members are also rather gossipy and happy to share their thoughts. If I'm lucky as a GM, the PC's start with a couple "innocents" who might suspect a person other than the murderer. Those first interviews might point places other than the BBG. Having the BBG deflect them towards another crew member (or even one mentioned by the others) won't be *that* suspicious given what they've already encountered in the first interviews. It can be a delicate balance, though - one group joked about wanting to sink the whole boat of miscreants.
My main frustration running the scenario is the captain's refusal to accept any evidence presented to him. Yes, it's in character given that the scenario suggests he's got a good chunk of the crew ready to be mutineers but it's incredibly frustrating for the players. One group ended up asking the captain if they could air their suspicions out over dinner, which worked out really well. The PC's presented their convincing evidence at dinner and ended up triggering not just the cook's encounter (she thought they were accusing her) but also the final confrontation. It was a wonderful resolution to the murder mystery- a dinner with courses of accusations, poisoned stew and fierce combat. The players loved the feeling of being in charge of the dramatic reveal.