For accounting in journal entry, create 3 more ledgers. SGST Payable, CGST Payable and IGST Payable.
In respective liability and asset ledgers whatever balance you have at month end transfer to these 3 ledgers. Once you make payment these ledgers will become nill and your respective ledgers will also become nill.
Normally the entry will be:
CGST 6% output Dr. - 1000
SGST @6% Output Dr. - 1000
CGST 9% Input Cr - 500
SGST 9% Input Cr - 500
SGST Payable Cr - 500
CGST Payable Cr - 500
When you make payment:
SGST Payable Dr. - 500
CGST Payable Dr. - 500
Bank A/c - Cr. 1000
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