Hi Tracy, please record the VAT payment manually against the return following the steps below. After this, you can match the payment in your bank feed. 

1. Go to Taxes and select VAT (Take me there).
2. Select the ▼dropdown menu next to the return.
3. Select Record Payment.
4. Select the bank account you've used to pay HMRC.
5. Enter the payment date and amount in the appropriate fields.

6. Select Save.