The discount function only works across the customer order lines, there is no function to apply the discount at the header level. We created a custom RMB function using a custom field on the customer order header.  The field sets the total order value - we refer to as the Net Lot Price.  Then executing the RMB function takes the sum of the Price/Curr values for each line and the compares that to the total in the Net Lot Price field.  The total order discount is calculated and then is applied to each of the lines in order to get to the Net Lot Price.  The individual line discount is recorded using the standard IFS functionality and appears in the discount field.  We also have an additional custom field per line that holds the actual Price per line at this discounted level.  This is the line price that the customer will see on the Invoice, and is also the value that would be credited per a line if an RMA was processed.  Nothing out of the box.  This was one of the larger design feature changes we implemented on the Customer Order for our initial go live.

Another option is to use the charges tab and set a negative discount?

You can add an Additional Discount in the customer order header.  It must be manually entered, there is noway to have it fetched into the customer order header. Once entered it will apply to all your customer order lines. 

I like the functional solution of Anbouk as it gives the opportunity to add a text to the given discount as well. Next to this, you could turn this, with some effort, in something automatically as you could add the charge via an event.

Steve