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.