Magento current Issue: Currently we do not have the ability to add handling charges to orders that are shipped ground.
We wrote a catalog rule (shopping cart price rule) to do this however it is confusing customers by showing discount. Here is the formula that needs to be implemented. Please let us know if there is a way to do this or if a module needs to be purchased.
Ground = $5.00
It is ONLY free if over $125.00 and if under $50.00 there is a $5.00 handling fee.
Fed Ex real time rate shipping is fine no need to change this for the shipping items 2nd day and Standard Overnight.