Update to anyone interested
I've transited though Manila recently on a 16 hour layover.
When you land in Manila, go to transfer area to get your boarding pass validated. Once it is done, you can go back up to OhP validation and then immigration. Once these are done, you can leave the airport, no need to collect or identify the luggage. I've went out,caught a shuttle to T3 and walked to Belmont hotel. Stayed at Belmont hotel with their day use promo. Explored abit and checked out, back to airport. Once you have reached airport, clear immigration. Now you are at gates,this is when you have to identify your luggage. To identify you need to goto gate 4 and take a lift to G floor, where your luggage will be stored and security checked. Once it is done, wait at gates and board your flight.