When applying a customer payment to their invoice, I want to leave an amount outstanding but still allow their discount.
When I enter the amount paid in /amount to apply/ and it is less than the invoice amount, the payment discount amount on the bottom of the screen disappears.
I think you need to make apply full payment to an invoice within the allowed discount period to make the discount work. For example, invoice is 100, and you apply 98 payment to it. If the payment date is within discount set up in payment terms, a discount of 2% is applied and the invoice will be closed.
If you only apply 10 again an invoice of 100, no matter when you pay, BC won't give you discount for the above scenario.
Do you mean that you want to apply customer payment along with the payment discount but there is still an outstanding amount on the invoice after the application?
If I remember correctly, it does not work this way.
As long as the remaining amount after the customer payment is more than the allowed discount/tolerance amount, then the discount/tolerance amount will not be considered.