I haven't done it for this promotion, but in the past stay 3 for 2 nights or other equivalents have always worked out fine for me. It's credited when you check out and are only charged for the two. But keep the paperwork anyway!
A: I have always had the discount applied on the exitting bill. A quick desk visit will likely solve the issue unless the conditions of the discount (weekend days, Thursday - Sunday arrival,etc.) were not met.
If you read the terms and conditions of the reservation, it will most likely say that the third night is credited on checkout. My reservation had that language and when I finished my stay, it worked that way. No problem. Take a copy of your reservation with you just in case. Hope this helps.