How to adapt Apache configuration to OS X Server?

I'm trying to get Server working on a Mac Pro that had been very happily running a number of websites with the built-in Apache installation all the way up to and including 10.8.  Sigh.  Server has been a complete nightmare in a bunch of areas, but especially with getting the websites working properly.  Things are sorta kinda working, but I'm nowhere near where I was before.  Maybe someone here can help...
Here's how things are set up:
My Apache config files are still in /etc/apache2 -- the main stuff is in httpd.conf, with a number of site definitions in /etc/apache2/other; these get loaded through an include statement in httpd.conf.
I've created entries in the Websites section of Server pointing to the sites.  I've left the sites' files in /Library/WebServer/Documents where they used to be, and pointed the server entry to those files via the "Store Site Files In:" option.  In the cases where the domain name is something like example.com, I've set up the "Domain Name" entry in Server as www.example.com.  I've then added "example.com" as an "Additional Domain"
What's happening is that the "www." versions of the sites are getting found and presented, but the basic domain doesn't work -- visiting www.example.com works, but visiting example.com doesn't.  In addition, some of the sites have nontrivial (and necessary) stuff in their config files -- redirection and the like -- and it's clear that the things specified there aren't happening.
So, as a first guess, it looks like the config files in /etc/apache2 aren't getting read, or interpreted, or whatever.  If this is meant to be a real web server tool, surely there's a way to handle custom Apache configurations.  Does this may sense to anyone?  Are there any clues out there?  To my eye, getting this stuff working should have been trivial, and it's been nothing but a nightmare.

Hi Jim,
I've had similar problems with OS X server but have gradually overcome them all, through working out the 'intent' of the developers.  My main reason for installing OS X server was to take things back in house after one of my commercial sites got hacked.  With a very Apple-centric household, I thought it would make life easier with tools like Profile Manager. 
If you we're to ask me my reasons now, I would probably say its that I refuse to be beaten as I have spent so much time getting it right.
The good news from your point of view is that there are loads of people like me within the forums who can help with whatever ails you!
My config is as follows:
OS X standard Apache and Postgres
PHP 5.4 with additional modules for imap integrated with OS X Apache but never to be clobbered by OS X upgrades.
MySQL via homebrew.
Running on OS X server.
Domain1.com - OS X wiki server
  - Roundcube Webmail installed as a webapp with MD5 auth ( can be attached to any website domain this way)
-   Webapp for Reverse proxy to an Ubuntu Server instance running under Parallels VM on same machine (different IP address) providing UPS monitoring and shutdown of all machines on network through NUT and SNMP monitoring via Cacti. My particular UPS's (Powerware 5110 x 2) USB driver not working under OS X power management nor NUT under OS X.
- 2 minecraft servers for my son and his mates!
Domain1.com.au - commercial site running Drupal CMS  / Postgres
Crm.domain1.com.au - SugarCRM CE 6.5 / MySQL integrated with OS X mail and calendar server.
Web mail via webapp
Domain2.com.au - commercial site - HTML
Webmail via webapp
Why not list what you are trying to do and what's not working and we can try to sort it out.
Cheers
Gerry

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