When you cannot fill an order completely, send what you have. The rest stays outstanding and you ship it when the stock arrives.
Ship what you have
Open the order and click the Shipment tab.
Click New shipment.
Click Expand all, or click the line you want to ship.
Type the quantity you are actually sending into the box for that bin.
Click Commit, then work along the stepper — Pick, Pack, Ship.
The form suggests everything by default. Typing a smaller number is how you short it.
Ship the rest later
When the stock turns up, open the order again and click New shipment. The form shows what is still outstanding — a line reading 0 / 14 has 14 left to send.
An order can have as many shipments as it needs. Each one is listed under Past shipments so you can see what went when.
How to know it worked
On the Shipment tab the line reads Partial, with the quantity split across Shipped and Remaining. The order stays In process until the last of it goes, then turns Fulfilled.
A line marked Blocked
Blocked means there is nothing available to pick — the stock is not there, or it is already committed to another order.
Check the item's available quantity before assuming the order is stuck. See Why can't I commit this order?.