Transit visa for Yangzhou?

We want to visa Yangzhou on our way from Japan to Taiwan, but it looks like we must enter the country through Nanjing airport to get the 144-hour transit. Is it possible to book a flight itinerary from Tokyo-Nanjing-Yangzhou, but get the VISA while we’re stopped in Nanjing? Or will we need to book the flights as separate legs in order to “Enter” at Nanjing, THEN separately fly to Yangzhou? Thank you in advance for any advice.