RE: the post from MaryLandT above is in error where it says "In QuickBooks, payments are applied to the overall total of an invoice, not per line item."
Yes, that is conceptually incorrect, a common problem among Intuit reps here on the community.
While you can't control how a payment is applied, it is more accurate to describe the case as the payment being applied on a pro-rated basis across the invoice line items, and also to the invoice total in its entirety, to reduce the open balance, which is tracked on the AR accounting row.
The way it's applied can seem convoluted when there are credits, discounts, and other special case line items on the invoice, but it's quite predictable and accurate.
