Cheers mate,
I can't help you with Age of Pirates, because I never played that. So what I write is for PotC:
Recruit officers at the tavern.
Then go to "Passengers" menu.
There, lower right corner of screen, you'll find a switch to "change officers role".
Fighters would be the ones that join you, keep them in your team of 4. Only those will directly fight with you.
If you don't want to risk your officers of this team in boarding operations, talk to them. Tell them "to sit out the next boarding".
All other officers won't fight, but still contribute their skills to yours in see combat. In example, a good gunner will improve your ships gunnery, even if not in your team of 4.
Same for a good merchant, when you do trade.
Switching ships is easy. Go to ship menu, select "ship transfer", select the two ships between you wish to transfer, in your case, Pearl and Ducthman, and then "switch ships".
Means, you'll find yourself on the other ship then.
Hope that helps.