49A. Notwithstanding anything contained in section 49, the input tax credit on account of central tax, State tax or Union territory tax shall be utilised towards payment of integrated tax, central tax, State tax or Union territory tax, as the case may be, only after the input tax credit available on account of integrated tax has first been utilised fully towards such payment.
So after insertion of this section the GST liability of IGST , CGST, SGST first will be adjusted against IGST and after that in any balance will be utilised against respective input ie. CGST or SGST. For example if IGST liability is 50000/-, CGST liability is 40,000/- and SGST liability is 40,000/- and Input credit available in IGST is 1,00,000/-, SGST Input is 50,000/- and CGST input is 50,000/- than first IGST input of Rs. 1,00,000 will be first adjusted against 50,000/- IGST than 40,000/- CGST and balance 10,000/- against SGST. So this sequence which was incorporated in new section which is effective from 1st Feb 2019. Further CGST liability can be adjusted against CGST input and SGST liability can be adjusted against SGST input and CGST and SGST liability cannot be adjusted against each liability.