I have a method in WCF which has a return type of Message as well as the input as message whcih type of binding will be used for this...what will be the service model in my config file
The binding specified for the service (i.e., WsHttpBinding, NetTcpBinding, etc) is applied to the whole service, not just specific parts. Nor can you have a service that has different bindings for different parts.
I.e., you can't have Service A with a ServiceContract using WsHttpBinding, the DataContract using NetTcpBinding, etc.
You can have Service A expose different endpoints with different bindings, but the point is the binding applies to a given service as a whole. It's the B part of the ABCs of WCF - Address, Binding and Contract.