Drupal 6.14
Fckeditor module 1.4
fckeditor 2.6.5
ckfinder 1.4
http://www.mydomain.comhttp://www.yourdomain.com
/sites/default/files/mydomain/me/
/sites/default/files/yourdomain/you/
administer>site configuration>FCKeditor>---choose some profile--->file browser settings
$baseUrl = '/sites/default/files/';

Re: CKfinder + Drupal + Multisite setup + Multiuser
You can reuse it in CKFinder in config.php.
There are two variables that can be used as $baseUrl and $baseDir: $fck_user_files_path and $fck_user_files_absolute_path.
Note that the algorithm that is used there to find the bootstrap.inc file may fail, check if it works as expected and if not, then simply set the $drupal_path variable to the right path and $bootstrap_file_found to true.
Wiktor Walc
CTO, CKSource - http://cksource.com
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Re: CKfinder + Drupal + Multisite setup + Multiuser