Before a Special Order will be available for final pickup, it must have an item received and matched to it to fulfill the order.
It is impossible to pick up a Special Order unless an inventory item has been matched to it.
There are two ways to match an item to a special order: Automatic Matching and Manual Matching.
In either case, once the Special Order item arrives at the store, it should be added into inventory just like any other item through Inventory > Items > Add.