Adding Extra sites folder to OS X Server that Server.app won’t destroy

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>

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>

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