Q: Where are the index pages & sub-directories supposed to be? In /var/www/clients/client0/web1 or under /var/www/clients/client0/web1/web folder? Where in ISPConfig is this specified?
A: in the /var/www/clients/clientX/webY/web folder. Specified in the vhost file. You probably dont want to change the default setting there, but i think in the apache directives you could change the Document root for the vhost.