[shinrai]

How much time in total? It sounds like you already know what you're doing. You'll be totally fine in Makati and Boracay.

Those unsafe places noted above are the Muslim areas in the south. Nobody goes there.

In Manila start off in Makati. Safe, nice, comfortable. Use that as your home base. Manila is a big city so there's a lot to do.
People might tell you Boracay is too touristy but don't listen to them. It's easy to get a flight in/out. Short runway and an exciting flight.
In Boracay splurge for a night or two and stay at the Shangri-La at the top end of the island. One of the best places I've ever stayed. For normal nights the Regency will do. Rent a scooter to get around the whole island. Visit the butterfly farm to play with the bats, kite surf (or take lessons) on the east side, visit Manny Pac's arena to watch the cock fights (part of the culture over there), tons of beach stuff to do on the cheap. After sunset walk up the main beach through the beach fronts of the nicer hotels for an awesome dinner on the sand. Oh yeah there's also this place called the Hobbit House...the Philippines is a different place. Have fun over there.