I have a credit on a customer invoice.
Sometimes you will have a customer that will over pay. Here is how you can handle that and keep your numbers straight.
First create your invoice like normal and save it with out paying. When you click "add payment" add the payment in the amount your customer is giving you. This will be an overage.
When I look back at my invoice list I will see that I owe her $1.67. I can also see this in the "Outstanding Balance Report" in the report section under the finance report heading.
Back to the invoice list and I see that I owe her $1.67.
Next time she orders, create an invoice as usual. When you pay the invoice add the overage in as a separate payment type. Mark that in your memo.
(You could skip the previous step and just enter as one payment. But if you complete this step you will have an audit trail of your transactions.)
Now add the rest of the payment.
Last go back to the invoice that had the overage. (If you forgot what number that was you can go directly to it from the Outstanding Balance Report.) Click "Add Payment" again and choose to add the negative amount. This will clear out the credit on her account.
It is a good idea to regularly check your Outstanding Balance report to know from whom you need to collect payment and who you owe.