For Councils working in Receipts & Payments, you only need to enter the opening VAT balance under Setup → Bank Balances. If you're owed a VAT refund from HMRC, you should enter it as a negative value by placing a minus sign in front of it.
If you're working in Income & Expenditure, besides entering it under Setup → Bank Balances, you will also need to include the opening VAT balance under Setup → Restate Last Year → VAT. The sign of the VAT balance should be the opposite of that under Bank Balances. In other words, if you entered a negative figure under Bank Balances, you should enter it as a positive figure under Restate Last Year, and vice versa.
This process ensures that your VAT balances correctly flow into your financial reports and that Scribe correctly tracks the VAT that you owe or are owed throughout the year.