1. Modify the relevant EDI schema and preferably modify the namespace to differentiate it from standard schema. Deploy it.
2. Go To-->Biztalk Admin Console-->Parties-->Select Partner--> Right Click-->EDI Properties-->Click on "Validation and ACK"-->Check "Extended Validation" (Image below)
Checking "Extended Validation" tells Biztalk Engine to validate against the custom schema validations. This is in addition to standard EDI schema validations that come out of box.