To do this with a calculation you would need to start out by making sure you have the baseprice, saleprice, and discount columns in your cart. Once those are present you can craft the calculation.
calculation for itemprice
WA_eCart_IIf(([Discount] = 1),[SalePrice] ,[BasePrice])
This calculation says if the discount column is 1 use the sale price, else use the base price. You would also want to edit your total total price calculation to work with the itemprice rather than the standard price.