The Novel's Title
Rudyard Kipling's title says that there is more than one captain here.
Do you get the idea that Kipling portrays Manuel as the second captain on board?
Manuel takes the spoiled brat Harvey under his wing - while the rest of the crew (except the cook!) rejects the kid - and teaches Harvey how to become a good - and caring - man, all the while showing Harvey "tough love".
For example, after Harvey sabotages the net so that Manuel can win his fishing bet with Jack, Manuel tosses overboard the prized halibut that Harvey had just hauled in. Manuel was teaching the importance of honest behavior, even over a small competition between co-workers.
E pluribus unum