Chinese Transit Visa

Hong Kong-Shanghai-Hong Kong does not qualify. Indonesia-Shanghai-Manila does qualify if those are the only stops. Separate tickets are ok.

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 is acceptable?

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

Hong Kong-Shanghai-Manila is fine. It doesn't matter how long you stay in Hong Kong or Manila. You don't even need to leave the airport. The only thing that matters is that your flight TO Shanghai takes off from one country, and your flight FROM Shanghai takes off to a different country (Hong Kong counts as a "country" for this purpose). It is a waste of time to contact the airline in advance. Just print your confirmed ticket to Manila and show it (if asked) when you check-in/board at Indonesia and/or Hong Kong.