@btks 

"The lack of percentage rates in line items means QBO is not an option for us."

It seems like a lot of work to find another system just for this one item when it can be easily done in QBO - it's just different than Desktop.  The only thing that QB Desktop does is automate the percentage calculation when you enter the discount line item after the subtotal, correct?  

In QB Online, all you need to do is subtotal (even easier than Desktop IMO - just click "Add subtotal"), then enter a Fuel Surcharge line item (same as Desktop), and in the 'Amount' box, you just need to enter the equation, and QBO will do the calculation.  For example, if you have $125.25 in fuel and want to add a 10% fuel surcharge, click "Add subtotal" after the fuel cost of $125.25, then add a line item called Fuel Surcharge - 10% (or whatever you call it) and in the Amount box type 125.25*.1.  That's it.  It will look the same as Desktop unless you're doing it some other way, which maybe I'm missing.