When using the Special Order items feature it is usually best to force serial number for better tracking (although not required).
Be sure the item has no inventory on-hand
Create a new invoice, add the item to the Materials tab and Save the Invoice
Under function choose Create Purchase Order:
Select the Items to order and click Order Selected Items
The newly created PO will pop-up, select Post Order from the menu.
In Physical Inventory you will now have an item On Order flagged as Special Order
Return to the Purchase Order and choose Receive Product from the Functions menu:
Receive the quantity and enter serial number (if flagged as Serial Required). The Physical Inventory item will now show as available and Linked to an invoice:
Return to the original invoice, and you will see the serial number you received:
You can now receive payment and post the invoice as usual.
RETURNS
When a serialized special order item is returned...
The physical inventory item will now show the item needs to be returned (special order items don't usually go back into regular inventory and would need to be returned):
You can browse all items that need to be returned by going to the Physical Inventory browse and selecting to search Need To Return: