You should just follow the normal flow:

1. You created a RFQ and sent it to your supplier
2. He confirmed that he can supply you in certain quantities and prices. Therefore, you validate the RFQ into a PO.
3. You receive the product or service you ordered and it contains a bill that shows additional freight fees that you didn't have on your PO. Therefore, on your PO document, you click on "Receive Invoice"; it opens a draft supplier invoice that you should edit and add a line for the freight fee. You should create a product called freight if it is something you want to track in analytics or analyses, otherwise just a description.
4. You validate the draft supplier invoice into a supplier invoice.

I didn't talk about the payment in this flow because it depends on your policy: it could be before receiving the goods (or service) or after.