Edit
/Library/Server/Web/Config/apache2/httpd_server_app.conf
Look at the bottom for
<IfDefine WEBSERVICE_ON>
Include /Library/Server/Web/Config/apache2/sites/*.conf
</IfDefine>
Include /Library/Server/Web/Config/apache2/sites/*.conf
</IfDefine>
Add a path to the customer Virtual Hosts folder
<IfDefine WEBSERVICE_ON>
Include /Library/Server/Web/Config/apache2/sites/*.conf
Include /Library/Server/Web/Config/apache2/customsites/*.conf
</IfDefine>
Include /Library/Server/Web/Config/apache2/sites/*.conf
Include /Library/Server/Web/Config/apache2/customsites/*.conf
</IfDefine>
Make a site in Server.app, then move the .conf file to the new location.
If you are using a custom port add
Listen *:8100
at the top of the .conf file outside of the VirtualHost sections