This is not easy to do in AX. It's such a common issue referred to as landed cost or import costing. There are a few addons available to handle it correctly.
The only way to do it in standard is quite manual. You have to create a misc charge which posts to the ledger. (Debit item or freight ledger expense account, Credit a Ledger account which you will use to clear out to a vendor invoice manually).
Then you can add the misc charge after you have posted the PO invoice. To do that, go to the Invoiced PO. Go to Inquiries button and view the invoice. From there you can add misc charges for the freight but it will post to the ledger clearing account not the freight vendor.
Then you need to go and clear out that ledger account and post it to the vendor invoice for freight.
Landed cost addons will help you allocate the freight across multiple POs based on different methods such as weight, quantity, cost etc. They will also let you post directly to the vendor account rather than going through the ledger clearing account.