Is there a special place for the roots website(your companies site) to go? Could i just make an account and just make the site off of one of those. Thanks

Depends on where you are going to put it and the software being used. if you are putting your site when other virtual hosts on the server, then just create yourself an account. If you have your own server, you can either use your control panel software like plesk or cpanel or you can just use the default web server installation, sometimes in /home/www/public_html or /etc/httpd/www/

it could be anywhere depending on your install.

I would keep it separate if possible to prevent any funny business.

In CPanel you just make an account. I don't know another way...