The Application Catalog and Software Center work hand-in-hand. The Application Catalog provides a list of optional applications you could choose to install, while the Software Center shows a list of the applications you've selected to install on your computer.
You can think of the Application Catalog as a store and the Software Center as your shopping cart. When you find an interesting title in the Application Catalog and click the Install button, it is added to your list in the Software Center.
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