Do I need two 144 hour entry visas

This is "Best Of Japan Cruise" provided by Royal Caribbean.

You will be eligible for visa free transit, but you should keep in mind that your flights to and out of Shanghai are not allowed to have any additional landing of any kind in both mainland China and in Japan!

You will easily find out your visa free transit option. You have to calculate the entire transit time, from your scheduled arrival in Shanghai (by flight or cruise) until your scheduled departure (by flight or cruise). If your entire transit time is less than 24 hours, you will be eligible for 24 hour visa free transit and if your entire transit time is longer than 24 hours, just for a minute, you will be eligible for 144 hour visa free transit.

I assume that you will be eligible for 144 hour visa free transit during your first stop in Shanghai and for 24 hour visa free transit during your second stop in Shanghai. Anyway, to be certain, you will calculate it in the way, I have explained. In nay case, regardless of 24 or 144 hour visa free transit, this is more or less, the same thing for you because your entire travel will be absolutely visa free.

By the way, you should use correct terminology. It is not 24 or 144 hour entry visa, but 24 or 144 hour visa free transit or better to say, there is no visa all. You will just approach 24 or 144 hour visa free transit counter in Shanghai, fill out a relevant form and shortly after, you will be allowed to exit the airport free of charge, visa free.