You will need to set this file in order for the File uploading to work correctly
fckeditor/editor/filemanger/connectors/php/config.php
$Config['Enabled'] = true ; - this is set to false when first installed - set to true as shown
$Config['UserFilesPath'] = 'http://yourdomain.com/fckeditor/mediafilesimage' ;The hard coding of this is set to the location of where the uploaded files will be - fckeditor will name the directories you set here and set the proper permissions of 777
$Config['UserFilesAbsolutePath'] = '/home/account/public_html/cfckeditor/mediafilesimage' ;This is the server root level for the server account.