Hi Sharron, thanks for joining us here on the Community
If the second payment is showing as an unapplied payment on the suppliers' account, then you can follow the steps below to match this to the refund in your bank:
1. Click + New > Bank Deposit
2. Choose the correct bank account and the date when the money hit your account
3. Scroll to 'Add funds to this deposit' and change the 'Amounts are' to 'No VAT'
4. Under 'received from' choose the supplier, for the 'account' choose Creditors, enter the amount & save
5. Go to the supplier's page and select New transaction > Cheque
6. Tick the deposit against the unapplied credit payment and save
7. Return to the banking screen to match
If you have not yet recorded the overpayment, you can do so by returning to the original bill payment and editing this to the full amount paid - this will then create the unapplied payment on the suppliers' account. Please get back to us below if you have any Q's!