If you are purchasing goods from SEZ, there can be two cases: SEZ Exempt or SEZ Taxable
In both the cases, you need to select Interstate regardless of supplier place of supply.
In case of SEZ Exempt, no tax account will be selected.
In case of SEZ Taxable, you need to select IGST tax account.
1. While making purchase, select Purchase SEZ Exempt
2. It will be reflected in GSTR3B in Exempt section.
1. Make sure you have selected default tax account in item
2. Select SEZ Taxable while making purchase
3. It will be reflected in GSTR3B and GSTR2