Double Visa

Your first itinerary is eligible for 144 hour visa free transit since 72 hour visa free transit option is not any more actual for Guangdong province.

Please, have in mind that the trains are not eligible for this option, but a through bus is. Anyway, you will have to book a bus ticket that clearly shows that your journey is from Guangzhou to Hong Kong. You will have to print out the bus ticket and have it with you in a hard copy. Beside the bus, I suggest you to take a ferry (catamaran) provided by CKS (Chu Kong Passenger Transport) from Shekou port in Shenzhen to Hong Kong. The same is valid as far as the ticket is concerned.

Your second itinerary is also eligible, this time for 24 hour visa free transit, but have in mind that you will have to fly from Hong Kong to Guangzhou to be eligible for this visa free transit option. Also, you should carefully count your hours from your scheduled landing in Guangzhou until your scheduled departure from Nanjing. The entire time has to be less or equal to 24 hours otherwise, you will not be eligible for 24 hour visa free transit.

Can we stay at any hotel of our choice on 144hr or 24hr visa? Or does it have to be a selected hotel and meet specific requirements?

Definitely of your choice. Also, it is definitely of your choice where will you go within the designated area and what will you do.