Multiple Shipments
You can make multiple shipments for fulfillment orders. Be sure not to mark the option Order Is Complete when shipping until you no longer wish to add shipments to an order. Add shipments to orders by going to Income -> Orders -> Ship Order.
You can invoice shipments separately as they are created by going to Income -> Orders -> Fulfillment Order -> Orders -> Invoices, or you can invoice multiple shipments into one invoice by waiting until all shipments have been made, then convert the order to an invoice.