Mandalay-kunming-nanjing-tokyo, tokyo-PVG-Kunming- Mandalay

I have overnight layovers in Nanjing and Shanghai. Will I be able to use the 24 hour no visa transit? I leave the country less than 24 hours after arrival. When and where will I go through customs? Though I will be arriving on a domestic flight Kunming to Nanjing will I be able to go through customs to exit the airport or do I need to request the transit visa free in Kunming? If I exit in shanghai will I go through customs the next morning when leaving on a domestic flight?