Once you've received your customers money, they expect to be sent the products that they ordered. With the Shipping module (not to be confused with the Shipping Quote module), Ubercart can keep track of which products got sent where in which box.
The process starts by organizing products into physical packages, each of which will have a separate shipping label. This is done under the "packages" tab on the order's page. This page shows a list of the packages that have been created. If there are products that haven't been packaged yet, there will be a link to the "New Package" page.
The New Package page groups the unpackaged products by shipping type. For each product in the order, select the quantity and the package to put them in. If more than one product model have the same package number selected, they are all considered to be in the same package, even if they have the different shipping types. The shipping type with the lowest weight of those products becomes the shipping type of the package. Choosing "Sep." as the package for a product makes Qty. separate packages with one product in each.
Each package can be changed or removed through the "Actions" links in the package entry. Packages inherit their default shipping information from one of their products, so things will go more smoothly if shipping types for packages and their products match up.
Once packages have been made, shipment information can be generated for them. With the appropriate shipping method modules, this can include printing a label and scheduling a pickup. Even without any, the Shipping module can record origin and destination addresses, pickup date, estimated delivery date, package type, and other useful information. By assigning packages to individual shipments, it opens the door for other modules to extend the functionality through RMAs, damage reporting, etc. When shipping packages manually, the shipping types are not much more than hints, but the method modules may expect specific product information that may not be there if given packages of the wrong type.