When you say allowances - do you mean a discount? If not, can you provide additional information on what an allowance is used for in your company? 

It is a discount but not a cash discount.  A lot of our customers receive a damage allowance (percentage of the invoice), or freight allowance, etc.  They are all percentages.  The Marketing Director now wants this to be reflected on each invoice.  If it can't be automated, it would be entirely too time consuming to add a line to each invoice.

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.)  

You could use the discount field on the invoice or if the discount (allowance) is always the same you can add it to AR - Customer Maintenance - Tab #2 Additional - Discount Rate.

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.