You can either have your users create those folders with their email client, or you create those folders with ISPConfig when you create a new user.
For the latter, you'd have to modify the function user_insert() in /root/ispconfig/scripts/lib/config.lib.php.
In line 654 you could insert something like this:
PHP Code:
exec("maildirmake ".$web_path."/user/".$user_username."/Maildir &> /dev/null");
exec("maildirmake -f Drafts ".$web_path."/user/".$user_username."/Maildir &> /dev/null");
That would for example create a Drafts directory within Maildir.