You can set the partitions when you install your server.
Could someoen propose the partitioning schema for Ispconfig3 with
I would not make that many different partitions as you will sooner or later get troble with it if one partition gets full. But if you really want to make many partitions, make sure that you have a large /var partition as websites and email accounts are stored in /var (on ubuntu, debian, centos and fedora). Only on opensuse, the websites are in /srv