Entering any country on any yacht requires the captain to list you as crew or passenger.

Before leaving the territory, the captain also has to check you off of his boat or take you with him. Checking you off his crew list can be done when checking in with a copy of your plane ticket, or once you decide to leave, again with a copy of the plane ticket.

The immigration officers are pretty specific when it comes to crew check-ins and outs.
Customs has to do with the boat itself and goods brought in or purchased.