There are often multiple ways to do the same thing in AX which is good because you have a lot of flexibility. The same I true with business processes and relationships with suppliers. Some times you get one shipment some times two, sometimes one invoices sometimes two. The better suppliers you will be able to work with and reduce some of the variability. When you get multiple shipments and multiple invoices for a purchase order you can enter these in AX so you have a match to the relevant purchase order and receipt.
Here is a quick walk through.