I've never used OS X Server, but from what I can tell, one of the "benefits" is that it comes with GUI configuration tools, which save you from learning all the commands and editing tricks yourself.
As for which config file it uses, you can find out what DEFAULT file it will use by issuing a httpd -V on the command line. You'll see an entry in there about SERVER_CONFIG_FILE. Note that this can be overwritten on the command line (ie. you could say httpd -c /etc/httpd/httpd_macosxserver.conf) to start up with that file instead of the builtin default.
One simple way of finding out which one is used is simply to make some changes in the GUI configuration, save those changes, and then check the modification date of each file to see which has changed.