Here you can configure surcharges that you like to (automatically) add on orders. This could be for instance toll, waiting hours etc.
Navigate to Configuration > Order input
Click on General surcharges
You can configure for which customers or for which transport service that surcharge is applicable. You can also add the invoicing details so that the correct rate is automatically added on the invoice.
Be sure that you always link the general surcharge to a price list, and be aware that they need to be 'active' on the different transport services before the costs are added.