Since the PowerCMS dot release was upgraded to the new HTMLEditor and also was upgraded to use the KFM editor(Advance Upload) all the files are now stored under files/cms_files folder which is created the first time you try to upload any file to your server.
If you want to change where you want certain files to be changed, then under the HTMLEditor/editor/filemanager/connectors/php/ folder, open the config.php file.
At the bottom of the page, you will need to change:
$Config['FileTypesPath']['File'] and the $Config['FileTypesAbsolutePath']['File'] settings where your new location.