Links to the episodes for Naruto Shippuden are now up in the Naruto section. Not all of them are there, since I'm adding them as I watch. Don't worry, they'll all be there soon.
UPDATE: If you want to know when this section (and any other section) is updated, go next to your name (who you're logged in as), and click the link saying "RSS". This will allow you to have an RSS Feed directly from the site so that you know when something new has been added. This is very helpful with the forums if you're following activities there!