zPanel has had a rocky past as far as security is concerned. There are better alternatives out there, namely Webmin/Virtualmin. Or you could learn to do the Apache conf yourself, or even use the speedier nginx (my personal favorite).
This tutorial covers how to login with root, how to change the root password, how to create a new user, how to give the new user root privileges, how to change the port, and how to disable root login in. This tutorial is written for Ubuntu. When you first create your server, this tutorial explains the first steps you need to take. This tutorial is written for Ubuntu 12.04.