GST follows a system of ledgers for ITC and Cash. Both the Ledgers and Liability Register etc. are maintain online at GST common portal.
ITC availed by the taxpayer shall be credited to the ledger on filing of return and ITC utilized by the taxpayer for payment of taxes and other liability shall be debited from the ITC ledger.
Any payment made through challan gets credited to the Cash ledger and does not automatically get offset against any tax liability. Payment of taxes has to be made by the taxpayer by debiting the cash from the ledger and paying liability online.
The taxpayer will submit the valid return after payment of the tax liability arrived out of completing Return (GSTR 3 or equivalent one), through Cash Ledger and Input Tax Credit Ledger and file the return. The two activities (i.e. making payment for crediting in Cash Ledger and making actual payment of tax against the liability calculated in return) are separate activity.