VAT surcharges need to be accounted for as a cost in the profit & loss account (although any VAT surcharges you pay would be tax deductible when working out tax).
The journal entry required for any VAT surcharges incurred would be as follows:
Dr Penalties (P&L)
Cr VAT Control Account (Balance sheet)
The VAT control account in the balance sheet will then reconcile to the amount owed as per HMRC.