Sometimes I book through the 1-800 number (or one of the other numbers listed on the certificate if I'm outside the US), but if I'm somewhere where I can't get a toll-free call, I've booked a reservation on-line or through the property itself and called later to confirm that the rate is OK for Bonus Bucks.
You might give this a try. What has happened with me is that the CSR at the phone number will enter something into the reservation noting that I will be using Bonus Bucks (or Premium Pounds or Extra Euros) so that the property knows it has been OK'd when I check in and tender the certificates.