multiple upload directories

Could you explain a little bit what exactly do you need? You can configure as many directories as you want by creating many resource types pointing to different locations.

Enable session supportin config.php with session_start():

Then, in the configuration file, assuming that in the $_SESSION array a user name or id is available, use it to construct a dynamic baseUrl / baseDir variables:

$baseUrl = '/ckfinder/userfiles/'.$_SESSION['user_id'].'/';