Check this article for hints and tricks about traveling the Philippines
Ours was a bicycle trip of the Philippines of one month, the length of the Visa free regime.
As usual we think that a bicycle is the better tool to deeply explore, get in touch with the real and experience landscapes and people. Even though Philippines is an inexplicably underrated cycling destination, you should really consider the cycling option.
Anyway the itineraries listed here could easily be done by local transports or renting a scooter. Just click on the images to read the full articles, those include detailed interactive maps with elevation profile.