Below is a link to a thread talking about various ideas for handling Freight. Worth reading through if it give you some ideas.
We’re also in the same boat (with freight and change orders). We try to match the sales order with their PO’s for easy processing, but its a battle.
You could make a stock Part called “Change Order” and adjust a bunch into inventory at zero value. This would allow you to add “Change Order” as a line item on a SO, give it a price and a more detailed description, and just ship from stock along with the rest of the order (when it needs to appear on the invoice as a separate line).
When they have a separate PO number, it becomes harder to manage. There is a “PO Line” field on the Sales Order Line, which is MEANT to correspond to the Line Number on the main PO… but we’ve inserted secondary PO Numbers there. That value appears on packing lists and (I think) invoices. One issue is that secondary PO Number isn’t searchable from the SO landing page. But I think you can under the Customer > Activity > Orders because that list breaks it out by line item.