There are a few ways of handling this:
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Post the entire receipt to the client file to offset future bills. This pays the bills for the matter and leaves the client with a general retainer balance.
In Amicus Accounting 2008 or higher, the Enter Receipts function allows you to enter the total payment once. Select the bills to pay and any overpayment will be displayed as an Unused Payment. You have following ways to handle the overpayment:
Apply as a general retainer which can be applied at a later date.
Issue a refund check.