Chinese Transit Visa

I'm a Italian citizen. i will travel to Shanghai from Indonesia. but how if the flight to Shanghai require to layover in Hongkong. So the flight will be:
Indonesia - (layover in Hongkong) - Shanghai but within 72 hours have booked a ticket to third country, like Manila for example.
Actually I will go back to Indonesia, but via Manila. Do I need to stay in Manila for a day, to be considered that I will go to the third country, or Manila for transit before arrive to Indonesia is acceptable?
Even though just spend 2-3 hours in Manila, then reach flight to Indonesia.

And how do they know that later I will get the permission? Do I have to contact the airline first or shall be done at the Shanghai Airport?

thank you very much for your feedback