I just did this on a sailing with a friend I wanted to treat without her knowledge. The pre-paid gratuities show up as a credit for each person at the beginning of the statement, then each day the appropriate gratuity is debited.
The prepaid internet does not show, nor are any shore excursions that were purchased prior to departure.
I also checked in online for both of us, used my credit card number for both of us and told her we would settle up later. My friend is not ver good with technology, so she never really explored the Navigator app and did not come across the statement.
I think @dfish suggestion to say the prepaid grats were part of a promotion is a great idea!
Of course my friend knows me quite well and ended up e-transfering me lump sum shortly after the cruise anyway. Still managed to save her some money.