You will have to clear customs in Manila.
I just came in on PAL from Honolulu, arriving at 4:30pm at International T2, with a 2 hour layover. Was through immigration in 10 min, waited 20 min for my checked luggage (including a bicycle in a case). Took them over to Customs, was cleared and back to the luggage belt. Walked outside and up to Domestic (same terminal) where I was still an hour early for boarding my Cebu flight. Amazing.
I do this once or twice a year and it never takes more than an hour to hour and a half max. But that's assuming you're flying in and out of terminal 2. And it helps that it's all on the same airline.