Once you've got yourself a hefty amount of booty, sail into a port and the bottom left hand box will be divide the plunder. it splits the treasure up between you and your scruffy crew.
Tips for serious players: After dividing the plunder you lose your entire fleet except your flagship. So sell off every ship except the one you want to keep. fire as many crew as possible and sell all of your goods BEFORE dividing the plunder, to boost your $$$. also, if you want to keep playing you must click continue, as "Retiring" is exactly what is means. no more pirating.