How to record the VAT you paid to the authority
Once you pay the return, record the payment against it so the VAT accounts clear and the bank shows the money out.
Steps
Open the return
Open the VAT Return for the period under Reports → Tax.
Record payment
Under Payments to the tax authority choose Record payment (Record refund when the authority owes you).
Choose the bank
Choose the bank account the money moved through and add the payment reference.
Check what is left
The return shows what is paid and what is still due or still reclaimable.