How Can I Add a Handling Fee to Orders?
To add a handling fee go to System -> Configuration in the admin panel. Select Shipping Methods from the left navigation.
Here you will be able to add a handling fee to the real-time rates provided by UPS, USPS, FedEx and DHL, and even the predetermined rates that you can set up for Flat Rate and Table Rates shipping. Simply enter the value of the handling fee in the handling fee field for the carrier you want to update.
Select the Save Config button and the handling fee will be added to all the rates received from that carrier.