4u2dci4, it looks to me like you’re using the template that’s installed by default, and you’re just customizing it. You actually have complete control (down to every <div> and whatever else you want) by creating new templates or editing the code for existing ones.
MODx isn’t like Drupal or a lot of other CMSes because you don’t really have "modules" or "blocks" like you’re referring to. There’s no place in the manager where you tell it you want links on the right sidebar, a menu at the top, etc. It all has to come from you in the HTML you write. That’s the beauty of MODx, and it’s also why you need some HTML skills to use MODx well.
It sounds like you need a snippet like Wayfinder to do the links to your PDFs. The community will be glad to help you out, but do some Google searches for things like "MODx snippets" or "MODx Wayfinder", and you’ll find guides on how to get started.