If you have not created the over payment you can do so by following the steps in the guide below:
In Clear Books, payments can only be allocated to bills. Therefore, to clear an over payment, you would need to allocate the over payment to an over payment bill (which is just a normal bill with an over payments account code).
The refund you create to record the money back from the supplier would also be coded to this same over payments account code so that the over payment bill and refund effectively cancel each other out.
Head to Money > Unallocated Cash and click on Allocate link for the appropriate unallocated payment amount.
Click on the Create bill link to create an over payment bill (a bill with an over payment account code).
Fill in all the required fields for the bill and click on the Add link under the Account code drop down box.
Create a new account code, I have called this Purchase Overpayments.
Please note: the Account type to use should be within the current assets group for purchase over payments.
Scroll to the bottom and click the Save new account button. Then click on the Save button to confirm the bill.
Click on the Allocate payment button once you have ensured all details on the bill are correct.
Select the payment and type in the amount to allocate in the Allocate payment box. Hit the Allocate button to apply the over payment to the over payment bill.
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, this will be to record the refund.
Explain the payment using the Refund tab. Fill in the required fields and use the account code you created in step 4, in this case Purchase Overpayments.
Click on the Add new transaction button to complete.