I see that this post was never answered and it was 2 years ago. While it might be too late, or you may have found an answer, I will respond in case someone else has a need for it.
A vendor discount is a choice to reduce income, it is not COGS.
We have an income subaccount titled: early payment discount that we use to record this discounts.
When you use the "enter payments" transaction, you select the "discount button" to see if the correct discount amount shows. Your customer's terms must be set up correctly as Quickbooks looks at the payment date in relationship to the discount date to determine whether the customer is eligible for the discount.
