First, upload your PDF to the media library by going to Media > Add New (or open an existing PDF in the media library)
Open the item you've just uploaded and copy the URL to the clipboard, it should look like this:
http://www.mysite.com.au/wp-content/uploads/2015/11/my-file.pdf
Now, you just need to add it to the menu. You can add or edit items in the quick links menu by going to the following link:
http://www.moamagrammar.nsw.edu.au/wp-admin/nav-menus.php?action=edit&menu=3
This can also be accessed in the CMS by going to Appearance > Menus - then selecting the quick links menu.
On the left panel, drop down the 'custom links' section and paste the PDF URL you just copied into the URL field, enter the title of your menu item then click 'Add to Menu'
A new menu item will then be added to your menu at the bottom, you can drag and drop to move this around. When you're finished, click 'Save Menu'