Tracking numbers can already be put on completed orders, but you have to go through the process of packaging up the products and describing the shipment to Übercart. The "Ship manually" method lets you fill in all the information about the shipment like carrier, cost, tracking numbers, and package size. The tracking numbers appear on the order page in their own pane.

If that's more complicated than you really need, you can just put the tracking numbers in the order comments.