To keep costs down you should aim to travel through major transport hubs, as listed above. (gapyear.com)
While the first 2 have large cities which serve as major transport hubs (Manila and Cebu respectively), Palawan is compltely seperate. (philippinestravelpackage.com)
Other major transport hubs in the region include the cities of Gladstone and Rockhampton. (australia.com)