Plenty to do in Nanjing. I have tried every option from Pudong and the best is the airport bus that takes you to Hongqiao. I usually book my train ticket for about 3 hours after my scheduled landing in Pudong. I am often too early for the train so I try to exchange for an earlier train (free of charge) or I eat something at the train station. Not that some trains to Nanjing are much faster than others. Pay attention to this in the train schedules
I never had problems picking up tickets there. Watch this video: The hotel "in the city" is in the "new downtown area. A bit sterile and not much going on at night. But it is near the subway which the other one isn't. Probably a newer hotel as well. Both neither is great for tourism.
No need to have your return train tickets delivered to your hotel, pick them up with the other ones when you arrive.