I believe the latest versions of Ubuntu don't use an xorg.conf file anymore.
gertvdijk makes a good point, if you want to use a file to automatically configure your display setup it might be important to know what kind of card you have.
There might be a rather universal solution to this. Nvidia and Intel support configuration of your displays through
xrandr, meaning that if you could (i) save your settings to a file and (ii) automatically set that file as the defaults, you're good to go.
For (i), you can use
sudo apt-get install arandr and set your configuration. Through File > Save as you can save the configuration as a shell file. For (ii) you could of course load the bash file at boot, but this is an ugly solution I think.
You sound like you know what you're doing, deploying computers and all, hopefully this can give you a push in the right direction. If it does helps, please append this post to briefly explain what you have done to get this to work.
If memory serves me right, Nvidia allows importing and exporting of the monitor configuration through
nvidia-config. At least it did before they started supporting
xrandr. This might also be of use...