Page items with intelligent links to folders and contents

I’ve read so much about WordPress as a CMS and I’m familiar with Joomla. I’m setting up an intranet site in WordPress where my site has hundreds of PDF documents. I can’t find a way to link my pdf’s from my pages using a folder system – I’m using WP Media folder. I can go to the file and copy the URL but that doesn’t show the correct path to the document via the folder structure I’ve set up. Theses PDF’s are updated continuously and I’m used to updating the page, selecting the link to a new PDF and viewing the PDF thru an interface where I select the PDF and publish the page.
Would I be correct in assuming WordPress really isn’t meant to be used in this capacity – a large CMS? Is there a way to intelligently link from pages to a folder structure to pdf’s where there are frequent updates?
Thank you.