I've booked consecutive nights using free night certs where one came from my account and one from my wife's account many times. The reservations will be separate, with one in your name and one in your wife's name. You'll each have a unique confirmation number. When you get to the hotel just let them know what you've arranged and they'll take care of it. I've never had an issue doing it this way.

BTW, you'll earn points and a night credit for the night booked in your name and she will earn for the night booked in her name.