It's easy to apply a one-time discount to a wholesale order on RoasterTools:
You will see the discount field in the "Order" screen. You can enter in an exact dollar off (e.g. $1.00 per bag) or a percentage off (e.g. 5%).
You will see the discount when you click "Create Order" or "Update Order", depending upon whether the order had already existed.
If you'd like to use automatic discounts, you can learn more about those by visiting this article.