When entering the order's weight in the package size and weight column in the 'Incoming orders' screen, you should be measuring and entering the combined actual weight of your order's items, as well as the packaging used for shipping.
If you have the weight of your items configured in your Shopify store, then the total item weight (of the order's line items) will come through as the default weight in the application's pop-up. You will then be able to enter the final weight determined by the addition of your packaging.
It is important that this weight is entered as accurately as possible, as this will determine any potential surcharges when being handled by the carrier.
For further information on surcharges click here.
For further information on volumetric size and volumetric weight calculations click here.