I'm having problems with the protected file. I believe I have the correct path in the settings file because the setup.php said the protected path was ok. However, when I am not logged in, I can still get to our pdf files that are located in the $hiddendirectory.

Any suggestions??

Then you are not using fileprotection the correct way. Please read the instructionsone more time.

So I still have one question....

I re-read the instructions and understand how to protect the href link.

However, I still am not sure how to protect the files if someone types in the path into the browser. Also, search engines will still be able to crawl these files and we only want our users to actually see them. How do I protect the files in these cases where the path is known?

That's why you should use a hidden path so that no one can guess it or type it in. I suggest you put that directory outside your public_html directory or what-ever the directory where you upload your HTML files is called.