In order to get to Malapascua you first have to fly to Cebu. If you are traveling from abroad you can fly to Manila, and from there take a plane to Cebu; but I recommend flying to Hong Kong, Singapore or Kuala Lumpur, and from there taking a direct flight to Cebu.
Once at Cebu's airport you have different options. The easiest, and most convenient, is to arrange a pick-up service with your hotel in Malapascua. If you are traveling on your own, you can take a taxi to the town of Maya, at the northern most tip of Cebu (about 4 hours). If you want to save some money, and meet some friendly local people, you can take a taxi from the airport to the bus station in Cebu, where different companies run buses to Maya. I recommend you take an air conditioned bus.