Fair enough sorry, I will try to clarify all your points, I really appreciate you taking the time to tell me what I was doing wrong. I wil try to answer all your questions but please forgive my noob-ness if it shows through. I am trying to add a sudo user because the tutorials suggest it as a security measure and say to do all the set up work through the sudo user not the actual root again for security reasons. What is working right now (because I used the root user to set it up) is my two site configuration, one main site in the /var/www/ folder (which is my drupal site) and one in /var/www/example.com/public_html. It is the achieving of this set up that I seem unable to do as a sudo user, things like uploading via SFTP don't work as the sudo user and I am unable (even though I believe I am doing the tutorials exactly correctly) to achieve any sort of working config when using the sudo user, the closest I get is that I can have one site enabled at a time, the main or the virtual host, and whichever one I enable becomes the only working site at both domain names. It still sounds confusing I think. I am sorry I don't know how to explain myself better, its ok my sites are working now so lets just pray that keeps up lol. Thanks again.