Custom xorg.conf in 2.0.0.40

I have Shuttle Zen (st62k) that I have been using happily as a diskless Media Director, (and a diskless MythTV system before I discovered Pluto). Everything works well, but the ATI drivers do not support DRI on the Radeon 9100 IGP that is on this motherboard, where as the open source ones do. A such Video is choppy and CPU usage is high.

What is the correct way of having a custom xorg.conf for a system?

in 2.0.0.3x it was fairly easy to upgrade to xorg and have a custom xorg.conf as Pluto only wanted to mess with XFree86.conf

In 2.0.0.40 I can not convince Pluto that I do not have an "Radion 8500 or newer", (strictly Pluto is correct), and so Pluto continualy overwrites my xorg.conf. Setting the MD to use vesa or removing the device in Advanced->Configuration->Devices never seems to stick. I can only assume Plug-And-Play is getting in the way and setting it back durring the next boot.

I have tried editing the scripts in /usr/pluto/bin that seem to generate the xorg.conf and replaced fglrx with ati, which seems to give me what looks like a good xorg.conf and X starts OK, but the system no longer starts the Orbiter.

Any suggestions greatfuly received. I'll may end up finding a hacky answer at some point but I would like to know the correct way to do this.[/code]