Once all containers (or shipments) have been manifested and moved to their final shipping location, a shipment is set to "Loaded" status.
Warehouse Management > Shipments > All shipments 
Click Shipments in the toolbar and then click Confirm shipment to confirm the shipment. 
At this point, the miscellaneous charges are apportioned back to the order if the appropriate apportionment engine and shipment values (e.g., weight, value, volume) are set up.