prevent inbuilt apache running using server app
I had the same problem!

You have to edit:

/Library/Server/Web/Config/Proxy/apache_serviceproxy.conf


and 

/Library/Server/Web/Config/apache2/services/ACSServer.conf


Change "Listen ..." to "# Listen ..." (Change to comment).
This prevents the httpd from starting.

You have to restart after this!