Chrome automatically updates your installed extensions if they where installed through the web store. On the other hand, if you're using an extension that isn't posted there, you can manually add it to chrome, but you can't auto update the extension. You have to download the updated extension, open the extension page and drag/drop the new file there to update it.
Is there any way to auto update extensions outside the web store? I don't know if its possible to add the extension web as trusted URL for autoupdate or something like that, so Chrome would also check for updates there.