I seem to have had a different issue trying to book a pair of free night certificates. I called in and they looked up my certificate information, and booked two weekend nights at the hotel I had selected. However, from the confirmation it appears they just made a standard rate booking, and added a note about the certificates. It appeared in the confirmation email as follows:

BEST AVAILABLE RATE
Rate Per Night:
XXX-YY-2019 - XXX-ZZ-2019 XXX.XX USD
Total for Stay per Room Rate: xxx.xx USD
Taxes xx.xx USD
Total for Stay XXX.XX USD

Comments & Requests Additional Information
Guest will be using AMEX OFFER CERT: ANNIV #XXXXXXXXX/Upgrade NIG,HT #YYYYYYYYY . Thank you!!!!!!


From what is described here, this seems to have been done completely wrong. I'm assuming the best course of action would be to call back and ask them to attach the certificates to the reservation.

Update: After a call back to speak to another representative they confirmed that the prior booking was done incorrectly, and made a new reservation appropriately attaching the certificates. All appears to be in order now, and my booking information shows a "points" reservation that deducted no points from my account.