Hi TAYRN1
As the payment relates to a VAT period that is not accounted for in QuickBooks using the VAT centre you will have to create an expense. The payee will be HMRC, payment account will be the bank account you paid the amount from, enter the payment date, in the category section you will have to create an expense specific to this transaction, e.g. name it HMRC Expense, enter the amount and enter No VAT, save and close.
The above is only for this transaction and subsequently any VAT payments will be recorded in the Taxes section after you have filed your VAT.