I too am booking a trip to MNL and HAN. I ultimately used booking.com, after I narrowed down the geographic area of the city that I wanted to stay. Booking.com seemed to have the best rates. But I also check the property's direct site to see if there is anything that I am missing in terms of better rates. I also cross reference reviews with TripAdvisor, especially those 1-3 * reviews. Unless I see a pattern, I'll continue with the booking. (As an example, 1*, 1 time, because it took too long to checkout - I ignore it. 1*, multiple times because of billing issues - I'll move on.)

Safe travels!