When someone purchases merchandise, we want to offer them the option to have it shipped or to pick it up at our office since most come to our office regularly anyways.  If we set up a regular discount, it takes it off the base price, affecting the tax amount.  We want to be able to offer a discount for shipping people can input when they plan to pick up their items.  The best suggestion ET gives is to set up 2 items for each actual item - one shippable and one not - but this is cumbersome and confusing for the community.