Finding your way to the center of Palawan shouldn't be too difficult. The Puerto Princesa Airport is only 2 km from the city center, so it takes about 15-20 PHP to get to the hotels in the city itself by tricycle.
From El Nido Airport, the bulk of the island's visitors are picked up by jeepneys (a form of public transportation in the Philippines). These can be used to get to the local pier and then take a boat to your temporary accommodation.