new domain url for multi sites linked to sub domain drupal install
So finally figured this all out.

If like me you are weird and want to use a Sub-domain for your main drupal install and then create multi-sites from that you can just add your virtual hosts to the custom conf file or wherever you keep that. 

I found that to do away with .htaccess in favour of the /etc/httpd/conf.d/custom.conf file as well as httpd.conf on linux vps.

BUT if you want to add a new domain directing to same IP it will obviously keep searching for doc root,so even if you add the Drupal folder direction in virtual host it will just go there and not install at your actual URL.

So you need to create a symlink in this case and then add that directive to your virtual host. so it would be something like /var/www/html/drupal/nameofmysite.com  which would be a symlink to the actual folder in sites folder of subdomain.