The flights we booked were "straight" to Cebu and missing out Manila but there is no flight direct to Cebu from any airport in the UK. The best you can get is Heathrow to Manila, that is direct but Manila must be the worst airport I have known to get out of or changing terminals. I would avoid flying in to Manila unless your destinations is Manila.
Cathay Pacific has its hub at Hong Kong so we will be flying Manchester - Hong Kong - Cebu.
The last time I checked, there were only 2 International Airports in the Philippines and they were Manila and Cebu, so you are limited to what city you will land in and working your way from there.