If you're talking about the free night certificate you receive annually for the Premier card, just make a reservation online, specifying points. The system will automatically use that free night certificate; I just did this. Enjoy!
According to Marriott Rewards customer service on the phone, to avoid being charged points for the stay you cannot order these online. The system is not set up to recognize "pointless" reward stays, only stays that deduct points from your Marriott Rewards account. Not all hotels are included, the higher categories are excluded (cats 6-8 for the Visa Premier) and they normally expire within 6 months or at the most, in a year.
I agree with the others. Depends on why you got the certs. If they are credit card related, see Buffetter's response. If they are related to something else, then restate the question. Many of us get certificates for 3 or 4 different things. We will be happy to help. Just restate. Maybe include the code at the bottom.