Hi Midhun,
Are you going to use a PI or you go to connect directly the ECC with the endpoint webservice via SOAMANAGER?
Inside a PI you can set a field on the sender side to determinate with endpoint you go to use and in mapping level to map only the desired fields. I usually work with webservices with different strcutures, at least with the error responses and in mapping level you can do it without issues.
If you use somanager you can create two ports in that transaction and in ABAP level to prepare the XML's for request and response according the port to use.
Hope this helps.
Regards.