Hi Jontay,
You may want to check this map for your dive-destinations planning.
From Manila ALONE, without getting on another plane, there are already three possible areas:
Puerto Galera, as H20 mentioned (two hours road trip, one hour by boat)
http://www.atlantishotel.com/puertog...ettinghere.php
Anilao, Mabini (three-hour road trip)
http://www.aquareefclub.com/about.html
Subic (if you like WWII wrecks), a three-hour road trip as well
www.divebluerock.net/here.html
The links are potential point-people for your initial data-gathering but, really, once you get to the areas, you'll have your pick of places-to-stay and the local DM can group you with other divers anyway.
If you plan to get on a plane for the other islands, try to include Malapascua for the thresher sharks and mantas. I've got getting-there information in this story I once wrote for a travel magazine just for fun.