If you are using the Sales Order and Inventory modules, then you can assign a Discount Rate to the customer maintenance Additional tab that will automatically be added to Orders and Invoices.  However, you need to make sure all of your items have the checkbox "Allow Trade Discount" in order to be included in the discount calculation.  This will calculate a lump sum discount based on the total of all the items, that you will see on the Totals tab of the Order/Invoice in the fields Discount Rate and discount Amount.  If you want to manually update any existing sales order lines to be eligible for the discount, you will see a "Discountable" checkbox on the line item that you can check.  (That box will be checked automatically for any new orders you create after you update your items.)  

We invoice through Sales Order... we will look into this.  Can you have multiple allowances?  We have some customers who receive 5 different allowances!

No, there is only a singular discount filed.

No, there is only a singular discount filed.