Loading confirmation based on inputs from interface

Sales order entry is done in JDE. The confirm shipment part is to be done based on the actual loaded quantity. The data of actual loaded quantity is received from interface. What is the best way to do the confirm shipment of corresponding open orders?

One way of doing it is to insert the respective data in EDI F47131 & 47132. And run R47500. But, this is not usefull when the sales orders involve transportation (since r47500 do not update shipment status).

Second way of doing this is to insert the respective data in EDI F47131 & 47132. And run R47131 to change the original order quantity to actual shipped qty. And then run R42500 or R47500 based on SO type.