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Re:Mayflower 400: the science of sailing across the ocean in... by sdeer on Saturday September 19, 2020 @01:22PM (#24528999)
The crew (other than the captain who probably had his own cabin) probably stayed at the lower deck because the gun deck had better ventilation for the passengers. It took a long time after a ship first became visible for a gun battle to occur so the crew had enough time to get ready.
Re:Mayflower 400: the science of sailing across the ocean in... by pbalau on Saturday September 19, 2020 @05:49PM (#24530534)
Most likely the crew used the forecastle for accommodations [0] (as they always do). I don't think the well being of passengers was a big concern for the crew.

0. https://en.wikipedia.org/wiki/Forecastle