If necessary, you can process a partial payment against an invoice by setting the next payment field in the invoice record to the amount that you wish to pay. When you make a partial payment, the system will not default the discount amount into the next discount field (the system will only take the discount automatically when the invoice is being completely paid off (when the total of the payment and discount amounts matches the open invoice amount), and the discount date in the invoice is greater than or equal to the current date.
When you specify the next payment amount in the invoice and process a payment, the system pays the amount specified against the invoice, and it then reloads the next payment field with the remaining balance for the invoice.