You need to use inbound shipment costing (search "Shipment Costs as Delivery Costs" to find the SAP documentation).
PO should be raised without freight conditions. Goods receipt should be done via two seperate inbound delivery documents which are assigned to two seperate shipment. Individual freight vendors can be assigned to each shipment and shipment costing documents can be used to value the freight service (either manually of via pricing conditions).
All three LE documents (inbound delivery, shipment, shipment costing doc) must be in place before the goods receipts are posted are posted on the inbound delivery but the result will be what you are looking for.
I have used this at a couple of clients, the goods receipt involves quite a few documents but the results are good. If necessary you can have multi staged shipments and multiple freight vendors for each goods receipt.
