You would have to double check the terms and conditions provided for either the rewards certificate directly, or the terms and conditions set out by the particular car rental company that is allowing you to redeem the rewards.
*note: you can redeem American Express Membership Rewards Points for coupons/certificates for Avis, National or Enterprise.
... they wanted to know if they could use a different Avis Discount Code (AWD number) with the coupon number on the Amex certificate. I went to the Avis website and did a search for Amex MR (Amex membership rewards). (you would now have to go directly to Avis.com/amexMR ) I was able to find terms and conditions for this program that confirmed that one of the terms and conditions listed stated (under the terms and conditions link at the bottom of the the box to the right)
"Offer may not be used in conjunction with any other AWD#, promotion or offer."
You may find it easiest to contact a customer service representative, by phone, for the particular car rental company that you are going to rent with, and ask them if they can provide you with information on the terms and conditions specific to using American Express Car Rental Rewards Certificates with them in particular. The certificate itself may already contain rental car discount codes that are to be used with the Amex membership rewards.