Drupal 7 CKEditor and KCFinder, how to upload to private files directory
I found a solution that works at least in my case. I was on the right path... If you simply want to hardcode an upload path, you just need to configure two things in the uploader.php, the uploadDir where the files will be stored, and the Drupal URL where Drupal can find the private files, in my case:

// UPLOAD FOLDER INIT

    // hardcode private file upload path outside of web root, can't be configured through the UI that I could find
    $this-&gt;config['uploadDir'] = '/var/www/private_files';
    // hardcode the private file url that Drupal needs to be able to access private files internally        
    $this-&gt;config['uploadURL'] = '/system/files';


I know uploadDir already because that's where I've already configured private files to be stored. To find uploadDir, I linked to a private file already located in /var/www/private_files, then double clicked to see the first part of the URL on the dialog that points to where the root of /var/www/private_files is located.

The next thing I had to do was disable htaccess checking in the KCEditor config file (/sites/all/libraries/kceditor/conf/config.php) by setting '_check4htaccess' =&gt; false