Jonmully,
We are frequently charging for Motor Freight shipping, but it would work for Package as well. I have just created a "Prepaid Freight" Item as an Other or Service type item in QB. I could have done this in Method, but the synch creates this in Method as well.
This is just entered like any other line item in the Estimate, Sales Order, or Invoice. Just choose the name well as your user will need to know what to start typing to get the Freight line items to filter efficiently when entering the line.
You could create a bunch of Prepaid Freight Items, one for each state, or other way to have different amounts, or you can update the price on the Sales Order or Invoice when you get the actual freight bill.
It can be useful to think of ANYTHING you might want to charge a customer for as a Line Item. In many ways QB and Method treats ALL line items the same (calculation of taxes is maybe the biggest exception.) QB provides several Item types you can use including NonInventory, Other, and Service. I think for most purposes these categories don't really do anything in QB, but they can be very useful down the line. For example I put anything I want to Invoice the user but NOT see on a Packing list into the Other category. Anything I put into the Service category of Item type will also print on the Packing List.
And, finally, just remember that ANY item you have on your Sales Order, must be Invoiced or else the Sales Order will remain Open. As soon as all items are Invoiced, I forget whether by QTY or dollar amount, the Sales Order will automatically Close in QB, and therefore also in Method which helps you filter only Open Sales Orders.