Back ordering (if allowed by the retailer) is done inside your Accounting/ERP system. The Order Exchange analyses your accounting system looking for orders for the given customer/debtor that have the given trading partner order number. If the system finds more than one order that matches then it assumes you are back ordering. The system will continue to analyse and order until if finds no remaining 'open' or not shipped orders in the accounting/ERP system.
This means that to create a back order (or a multi shipment) you can invoice the items going now and create a second order (most accounting/ERP systems do this automatically) for the remaining items. You can repeat this process until you send the final shipment.
If you forget to create the back order as do so at a later date you need to come into the order exchange, find the order (which would more than likely be at completed stage), and right click then choose reanalyse.
If you need further information on this then please contact us at email@example.com