I set up that webmail-host configuration at my site and it works well.
# edit this vHost template in /root/ispconfig/scripts/lib/config.lib.php
# otherwise it will be overwritte on every host change in ISPConfig!
# This will be the default root for domains connected on this server
# but with no ISPConfig setup
# put in there a index.html like "this domain is connected - no homepage available"
this is the first virtual host setting in Vhosts_ispconfig.conf and will be overwritten every time you change host settings with ISPConfig - so you have to patch the config.lib.php near line 1231 - search for the textphrase "NameVirtualHost schreiben
now adding the subdomain webmail.* for every host on the system:
CustomLog /var/log/apache2/webmail.HOSTNAME.de.log combined
I dont know what happens, if you add a subdomain "webmail" directly in the ISPConfig Hostsetting. Look in httpd.conf which *conf-directory will be read by apache at first. I think the first *.conf wins the match ...
other virtual hosts in vhosts.d will work with the same procedure, e.g.
the index.html´s in that public_html - directorys redirects the users to the correct sites
and so the users only have to know the easy to type hostname like webmail.MySite.de or phpmyadmin.MySite.com and what ever you like.
hope that helps ....