How do I upload PDF files and link them in the body of my article page to download?

The easiest way to do this is to upload your files using the Media Manager. I suggest you create a sub folder called PDF within the 'Stories' sub directory, and store them there. You can then use the Media Manager feature which generates the correct URL to your PDF file when you select it and cut and paste this URL as a link in the appropriate place in your article page using the link button in MCE editor. This is simpler than installing DOCMan, document management for a few files. If you have a large number of files to maintain, then DOCman may be a better solution (see Chapter 8.3.2 of the eBook).