Hi Rick,

If the customer is okay with it, you can put the balance on their account.  You do this in the Receipts journal, but you have to make sure the "Enter Customer Deposits" button is checked in the toolbar; it is a picture of a safe with an arrow:

In my example above, the invoice was for $52.50, but the customer gave me a cheque for $60.  I input the $52.50 against the invoice, then record the remainder ($7.50) in the "Deposit Amount" at the bottom of the screen.  This gives me a total receipt of $60.00.  You can enter a comment if you want, such as "$7.50 overpayment on invoice X."  

Once you post the receipt, the deposit will show up in the list of invoices as a negative that you can apply to future payments.

I hope this answers your question.  Please post back and let us know!

Cheers,

Andrew

Andrew, this is great! Thanks so much! This solved my problem.

Awesome...glad I could help!

What should I do if my customer has paid an invoice twice and they do not have any open invoices?  I have tried to enter the second payment as a deposit amount but I can't post it because I get an error that says Transaction is not balanced...

I would close the Receipts Journal and start again. If a Customer has paid for an invoice 2x and the funds have been deposited to the bank account; you record the amount using the Deposit Reference and Deposit Amount Fields.