You can add handling fees within your shipping zone(s). To do so follow these steps:

• Log in to the admin panel of your online store.
• Click on Settings →  Shipping Settings → Setup Shipping Zones
• Click the "Edit" link next to the zone for which you would like to apply a handling fee.
• Scroll to the bottom and you will see where you can input the handling fee. Input the handling fee you would like to add to shipping charges next to "Add."
   

        Click Save.