Disable X Server Websites; Continue Using Apache


I installed OS X Server 5 on top of Yosemite. It's doing a good job for DNS and Mail, but it's NOT playing nicely with my websites. When I add any additional Apache directives to my .conf files, Server has a tendency to delete them for me. Apparently Apple Knows Best.

So, I want to turn this off and go back to running Apache without Server. I'm having trouble working out how to do that.

Obviously, I don't want to disable /System/Library/LaunchDaemons/org.apache.httpd.plist. I need that to start Apache.

I took a look at /usr/sbin/httpd-wrapper and can see that it's merrily deciding what to use as the config directory, but... then I'm stumped. "Something" is telling httpd-wrapper to use the config directory/files under /Library/Server. I don;t know where that "something" is?
Is there something I should delete? Or edit? Under /Library/Server/Web/?