I'm a Philippine passport holder but a have my permanent resident visa here in japan

You need to have a single entry Tourist L for visiting Shanghai and Guangzhou.
You need to prepare your valid passport, an application form, a recent taken photo, your hotel bookings, round trip tickets and permanent resident permit in Japan for the application. Since you live in Japan for a long time, you may need to apply the L type through a local tour agency and you can consult more information locally.