In Clear Books, payments can only be allocated to bills. Therefore to clear unallocated cash, the overpayment would need to be allocated to an overpayments bill. This invoice would then be reversed by creating a refund transaction.
Head to Money > Bank accounts > Unallocated Cash.
Click on the Allocate icon for the appropriate unallocated payment amount.
Click on the Create bill link to clear off the over-payment.
Fill in all the required fields for the bill and click on the Add link under the Account drop down box.
Create a new account code, I have called this Overpayments. Tick all the required check boxes.
Please note: Account type to use should be a current liabilities group for sales overpayments, and current assets group for purchase overpayments.
Click the Save new account button at the bottom once the account code is added.
Click on the Allocate payment button.
Select the payment and type in the amount to allocate in the Allocate payment box. Hit the Allocate button to complete.
Next head to the Money > Bank accounts menu and click on the Money in link for the appropriate bank account.
Fill in the details of the money in form.
Explain the payment using the Refund tab. Fill in the required fields and use the account code Overpayments.
Click on the Add new transaction button to complete.