If the product categories you created in Magento are not appearing in the top level navigation, do the following:
- 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.
- Go to System | Manage Stores and select your store name to edit.
- Make sure the root category points to Default if that is where all of your categories are built from.
- Make sure you re-index if necessary.