You can add more than one person onto your other 3 ships and all of
their scores will stack with that ships captains scores.

There are two different ways to do this

1) On the Open Sea screen (where you can see all of your ships) get
close to another of your ships and a swap cargo icon will appear. Go
into the swap cargo menu and there is an option to switch captains. 
Under this option there is a screen that has 4 slots, one of them is
the captain of that ship.  Click on one of the other 3 and then
assign passengers to each one.  When you do this the DISAPPEAR
from your passenger list. You will need to get more party members at
the tavern if you want to fill up all your ships.  DON'T sell the
ship with the other 3 crewmembers still on it.  You will lose
anyone that is still on board.

2) The second way to do this is to capture a ship and do it when you
assign a captain to the captured ship.