Setting up dual monitors in Ubuntu (Karmic) has been easy for quite awhile especially if you are using an Nvidia chipset. Using the nvidia-settings application allowed me to configure everything I needed. The problem was when I tried to save the configuration so it would persist when I rebooted. The utility said that it could not parse the existing xorg.conf configuration file.
There are two solutions to this problem. I found both in the comments section of a bug report describing the problem. The first option is to add the following to the “screen” section of the /etc/X11/xorg.conf file.
Device "Default Device"
This still gave me a few problems related to saving a backup configuration file before writing over the existing one, so I then used the next suggestion and ran the configuration tool with administrative privileges with the command:
gksudo nvidia-settings
Then it had full access to modify the configuration file. Now when Ubuntu starts up, the screen positions and sizes are maintained.