Clients have the option to allow their orders to be partially shipped. The partial ship option can be set on the company level so that all orders can be Partially Shipped, or one off orders can be set to "Allow Partial Ship" from the order level.
The order level option is not based on the customer set up. This setting is useful when there is a large order and the customer would like to go ahead and split ship the order, without having to wait until all back ordered parts have been received before it can be completely shipped.
To set an order to partial ship, go to the Order page, search for the order and select Partial Ship.