Is this your first trip to the Philippines? If not, please do not discount Boracay. It is stunningly beautiful, a nice mix of gay/straight, and crystal clear waters. You can walk everywhere, and you'll meet great people from all over the place. I have been twice before, and I am returning again in November. Manilla is not a very pretty city, and there is one gay area, although I forget the name of it. I am staying at the Renaissance in Makati, but I am sure there are cheaper hotels around. Have a great trip!
For domestic flights you'll need to go to
www.cebupacificair.com or
www.zestair.com/ph. Domestic flights are pretty reasonable.