If a product has a special price for a specific customer and that customer also has a discount applied to their accounts there is no setting in the Invoice and Orders Defaults discounts tab that works so that when you raise an invoice for that product with a special price for a customer who has a discount applied to them it will apply both the special price and the discount and not just the special price.

I have tested this and no setting seems to only apply the special price without the discount. Even though the text in the Invoice and Order defaults box says "Do not apply Quantity Discounts to Special Prices or customer price list prices"

I have been on the phone with Sage to see if i was missing something and they confirmed that this doesn't work.