I do think many of the hotel companies require you physically be there to check in and swipe your card. I know some folks have work arounds but if you don't swipe you may not earn.
If you have a relationship with a GM they can work with you on it but trying to do it via prepaid and no show can be risky.
As for not staying in the room that you check into, advising the GM or having a note on your account that you may be in and out would be helpful, although I have not done it.
If they get their revenue and you communicate, I suspect most GMs would be reasonable and work with you.