I think best decision would be to display a debconf question "Do you want to 
enable proprietary NVIDIA 3D video drivers ?" in .config script of nvidia-glx 
package. If user chooses "Yes", then .config script should run
 "nvidia-settings enable" and if it detect, that user's X configuration has 
been altered then it should display another debconf question:
"Warning: your X configuration has been altered. Proprietary NVIDIA 3D video 
drivers can be enabled automatically, but yours modifications to X 
configuration file (/etc/X11/xorg.conf) will be lost.
If you know how to modify X configuration file manually you can change the 
value of Driver in Section "Device" to "nvidia" in this file to enable 
proprietary NVIDIA 3D video drivers.
Do you want to enable proprietary NVIDIA 3D video drivers automatically and 
lost your modifications to X configuration file?"

If user answer "Yes" to this question then .config script should run
"md5sum /etc/X11/xorg.conf | sudo tee /var/lib/x11/xorg.conf.md5sum" and  
"nvidia-settings enable".

In any case .config script should check if user really has NVIDIA card,
supported by nvidia-glx package, AFAIL nvidia-settings script already
has this ability.

Btw, I think it's very easy to rewrite nvidia-settings script to work
correctly even if user modified xorg.conf - we just need to find Driver
in Section "Device" and change value to "nvidia" if there are several
"Device" sections then needed section can by found by value of BusID.

-- 
NVIDIA 3d drivers can be configured by GUI
https://launchpad.net/bugs/61844

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