Dataflow coding for different system configurations

I understand the concept of System Configurations where for each System Configuration I can put in multiple datastores in to a single package.   The problem for me is that some of my dataflows have SQL queries hardcoded down  to the [db].[SchemaOwner.[table].   So the dataflow works for one System Configuration but does not work for another.   How do I use pointers/variables in the SQL query so the query will work in any System Configuration?

Thanks!