For some reason I have 2 working but the one I really need, doesn't. I can log in to the FTP for it, but cannot connect via hostname. Would it affect my DNS/hostname if my server name and domain are the same? e.g. Server named - server1.example.com and domain for the site - www.example.com
This affects at lesat email but might also cause problems with the webserver. Your server hostname should something like server1.domain.tld but not domain.tld as we describe in the perfect setup guides. After you changed the server hostname, you should check that you selected auto subdomain www in the website settings (dont use auto subdomain *) and that the IP address of the domain in dns matches the ip address that you selected in the website settings.
