Hi Sethu,
If you can export the relationships from the application layer, than you import them in TDM and use them. Those relationships will only exist in the TDM repository but it does enable TDM do use them just as normal relationships from the db.
The import file needs to be in a csv format, for the correct structure, export the relationships from a database with relationships. That way you'll have an example at hand.
Not sure if importing relationships can be done in the portal already, if not that you'll have to use DataMaker or you could opt to do it by the API calls although that would mean more work.
Best regards,
Peter