Hi Nitin,
First of all you don't need 2 interface to achieve this .
.Create another message mapping in your 1st scenario only i.e source structure to IDOC structure.
.In you operation mapping include this message mapping after the first message mapping which you did for removing duplicated so that input of second MM will be output of 1st MM.
Br,
Manoj
Edit : Praveen was faster :)