If an invoice is only partially paid, how do I clear the balance?

It depends on weather or not you expect any more payments to come in on that invoice.
1) If you believe more payments are coming, just post the partial payment and do not mark the invoice as ‘Paid’. Then you can post more payments to that invoice and the invoice will remain on the aging reports.
2) If the partial payment is all that you are going to receive, simply
mark the invoice as paid.   When you settle the invoice, WinFactor will back out the unpaid balance from the rebate due for that invoice.

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