Rs.100 for CGST & Rs. 100 for SGST for everyday of delay after 20th september i.e if u r making the payment today (25/9/2017), ur late fees would be Rs.500 for CGST & Rs.500 for SGST [(25-20)*100]. So in total Rs. 1000.
No. GST 3B can be filed only after offsetting all the liabilities including interest and late fees. So, only after payment of late fee, 3b can be filed.