The Misc. Charges can be setup by clicking on the Misc. Charges in the Additional Order Options area of the Maintain order screen

When you click on the misc. charges, the misc. labor charges/details window will pop up:

On this screen you can add a percentage charge by selecting one of the percent buttons on the right. This will add the selected percent all line items in this order. 
To enter a Percentage discount you can double click on the yellow box in the upper left area of this window and enter a discount with a – in front of the percentage you wish to give. i.e. -10% will give 10% off each line item in this order.

You can use this screen to provide up charges for rush orders, or even provide discounts by using a negative number when you double click the percentage.

Send Promotional Materials: This is selected by default, however if a customer does not want future advertising info, deselect this box

Pricing Needs to be Determined?: IF CHECKMARKED this will prevent the order from being marked complete until the pricing has been determined and this box is unchecked.

Proof Requested: If a customer requests a proof for an order, check this box, now when you open up the order the next time, a message will pop up when you first open the order reminding you that the customer has requested a proof. This will also print on the work order summarizations to show you wish orders customers specifically requested proofs on.