If you want to charge the shipping/handling cost to your client you need to add it as a service product in an separate (last row) of the order.
To create the service in the account one should click the Gear Icon > Products > Add Product. Then, in the Product Type option the choice should be set to: Service. This service can then be added to a sales order and/or a sales invoice.
A similar process can be followed to add a cost (customs/handling/shipping) to a Purchase Order and/or a Purchase Invoice coming from a Vendor.