I've done this on numerous occasions. I book the rate and nights I want on the IC www-site. Then, upon receiving the confirmation, email the hotel and amb. service with the "Hi, mr. Voop here, I'll use the BOGOF for the second weekend night of this stay ref. XXXXX, please ensure that this be taken into account".

Usually I get 1-2 replies back of the "no problem, glad to have you stay with us, remember to bring your cert".

Getting to the property, I hand it over with the reservation. Never had a problem, although they may initially charge you for the night, then credit the card with the "free" night back.