You should refer to the documentation about this, but there are some common ‘gotchas’ that people forget to do:
• Go to Setup > Accounting > Shipping and enabling CHARGE HANDLING SEPARATE FROM SHIPPING
• If doing item-based handling fees, you must edit the item record for the item and add a value in Sales/Pricing > Shipping > Handling Cost
◦ Note that this field appears to be a flat value, and doesn’t seem to support multi-currency
• This item should be an inventory item
• You probably want to do this to the parent matrix item record so that the handling fee rolls down to all child items
• You must set up all shipping items that you want the handling fee to affect
◦ Go to Lists > Accounting > Shipping Items and edit every shipping item
◦ Once CHARGE HANDLING SEPARATE FROM SHIPPING is enabled, a HANDLING RATE subtab will appear on the shipping items
◦ If your goal is to charge additional handling for specific items, then you will need to enable HANDLING--PER ITEM
◦ If you don’t want to charge fees for other items (generally speaking) then you can set the default value to 0.00
◦ In the SHIPPING AND HANDLING RULES subtab, select an appropriate tax schedule for handling fees