/private/etc/apache2/httpd.conf is the correct 'master' config file for the Apache web-server when using Server.app
To have multiple virtual hosts on a single Mac server you either have multiple IP addresses defined and then define a website for each IP address, or have multiple host names point to the same single IP address (the more common scenario).
When a remote user accesses a URL with a host the webserver is able to detect which hostname they are requesting and then return the correct webpage. So if you have a list of websites like the following -
You can have them all in a DNS server pointing to the same single IP address of your webserver. In Server.app you define three websites on per host, and specify what folder full of webpages to use for each.
No need to mess about hand editing any conf files.