There is nothing special in this configuration regarding ispconfig, the only difference is that you have to explicitly allow access to the directory with:
<Directory /path/to/your/webmail/install>
AllowOverride All
order allow,deny
allow from all
</Directory>
and then add a alias for this directory. Ensure that you add your configuration after the configuration of the other vhosts is loaded by placing your additional config file in /etc/apache/sites-enabled and give it a name like 900-webmail.conf
were you instalelled your webmail client.
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