If the product categories you created in Magento are not appearing in the top level navigation, do the following:

  1. Make sure you created your categories and products under the Default category. Default has to be a parent, it's not just an example category.
  2. Go to System | Manage Stores and select your store name to edit.
  3. Make sure the root category points to Default if that is where all of your categories are built from.
  4. Make sure you re-index if necessary.