the ISP tools do not provide a way to look into folders or anything like that nor a way to know where anything should be uploaded via FTP.
WinSCP is an excellent tool for this. Not as good as having something builtin, but considering the cost of ispConfig, its a good alternative for now. You could suggest this in the bugtracker: http://bugtracker.ispconfig.org/index.php?do=toplevel&project=3
