You can keep the single configuration. The sample one has 2 of all because a 690 has 2 GPUs.

It looks like X is not starting properly. I'm not completely sure why this is.

Can you revert back to your old xorg.conf file, restart the computer and confirm that X is not running when it restarts?

It may also be an architecture issue. All the GPUs we tested were Kepler. I'll try testing it on a Fermi and get back to you.