[sdeer]

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.

[pbalau]

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