Hi there,
First of all, check if your root category is assigned to certain web-site and then under this root category you will be able to built-up correct category tree.
Also after that do not forget about flushing cache and doing re-index.
Read also this article on what should be checked -
http://www.mag-manager.com/i-cannot-find-see-new-category-categories-on-my-magento-store-what-should-i-check
As for products, they should be assigned to certain categories to be visible at the front-end. Also check their visibility, stock level, status. Get more details here -
http://www.mag-manager.com/i-cannot-find-see-new-products-on-my-magento-store-admin-what-should-i-check
If you will need to change any of the mentioned product parameters in bulk, you can use 14-day free version Store Manager for Magento application, as it has Multi_editor tool for bulk changes. Give it a fry -
http://www.magentocommerce.com/magento-connect/store-manager-for-magento.html
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Try out easy-to-use Magento Import/Export tool. A fully-functional 14-day free version of Store Manager for Magento is available for download here:
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Watch our new video on how to create Magento configurable products:
http://www.youtube.com/watch?v=KcHEV9ov8xg