How do I pay the balance to the captain?
Directly to the captain when the trip goes out, and cash in pesos is what most crews prefer. The exact balance is on your booking, so there should be no surprises at the dock.
Card facilities on a small boat are not a given here, and where they exist they often carry a surcharge from the operator's own processor. Cash in pesos is the smoothest way to settle up and it is what most captains and crews would rather have.
Your booking states the balance owed. Bring that amount, plus something for the crew tip, and the morning goes easily.
Draw the pesos before the day of the trip. Marina cash machines run out, particularly at weekends and in high season.