There have been recent threads about this worth searching for. My advice is ignore Metro Manila entirely for diving, especially in September as it is monsoon season in Luzon. It will take you at least 2-3 hours by land to get to any diving sites from Manila and those sites are so-so. Stay at the airport one night when you arrive, then fly to another island where the diving is great. Flights are around an hour to almost anywhere in the Philippines, and are cheap if you buy in advance. Sept 11 is pretty close so you may already pay almost double what you would have a month ago but still round trip is around $100usd in most cases. There are some to Cebu, Bohol, Dumaguete, and other places that have direct domestic flights from Manila, and some of those have international flights directly to them as well.
I am flying into Manila on Sept 6, staying overnight at the airport. Then flying to Cebu the next day, taking car to Moalboal, staying there 10 days. Then taking a car and ferry overland to Dauin, staying there around 10 days. Then flying from Dumaguete back to Manila, then flying right home the next day.