When you are in a course and encounter a document/PDF - to get past it: scroll down to the bottom of the page itself and check the box and click complete. You do not have to do anything special with the document (i.e. download/click/etc). The checkbox is not on the document itself, but on the website.
Here is a gif of how to do it: http://g.recordit.co/enB7CyIEc7.gif
Here is what you're looking for at the bottom of the page