After looking at your site, I'm still a little unclear about what you're trying to do. Are you trying to install Links so that your categories build http://www.yoursite.com/Category1/, http://www.yoursite.com/Category2/, etc. instead of http://www.yoursite.com/links/Category1/, http://www.yoursite.com/links/Category2/, etc. like it is setup now? Are you trying to figure out how to customize the index.html pages? Or, are you trying to get the index.html to automatically build with each category shown with that categories sub-categories shown under it?