Follow these steps
1.Create a Data Insight project
2.Create connection to ECC that contains the tables to be profiled.
3.Import the tables to be profiled
4.Create a Information Steward view to join the related tables together.Apply filter conditions if there's any
5.Perform the profiling on the view created in step 4
Look at IS admin guide http://help.sap.com/businessobject/product_guides/sboIS42/en/is_42_admin_en.pdf under topic "Using SAP applications as a source" for performance considerations.