I have a single-entry visa as an exchange student.

I am going to travel to the Philippines and Hong Kong in the beginning of January. I will return to Shanghai on the 25th, my flight back to my home country will be on the 28th. Do I need to apply for the 144 hour free transit BEFORE I leave to the Philippines, or upon arrival at Shanghai when I come back from Hong Kong on the 25th? I will then go to my university, pick up my belongings and go to Shanghai again before my departure. Do I need to register at the police station as well?