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In your Catalog–>Manage Categories, click on a category you have set up and under General Information tab, go down to where it says “Include in Navigation Menu” and select “No”. This will exclude this category from the main menu.
The left hand column is the layered navigation that kind of sorts your products by attributes. Check out this article here http://www.magentocommerce.com/knowledge-base/entry/tutorial-creating-and-managing-categories/