An item is considered "shipped" once an actual ship date is set. The Order Manager can be configured to set the actual ship date to the current date plus any number of days automatically upon importing orders. If this is the case, you will see quantities in both the Ordered and Shipped fields on the View Orders screen.
If you do not want to show that an item is shipped until you ship it via your shipping software or a drop-shipper, configure the Order Manager to automatically set the actual ship date after you import tracking numbers instead of setting the actual ship date upon importing orders.
Go to Main Menu>Maintenance Menu>Shipping & Fulfillment>Shipping Setup.
Under System Settings, click the Set Actual Ship Date after importing tracking numbers checkbox.
Click Save and Exit.