Installing drivers with two graphics card

I'm having troubles possibly because of two graphics cards. I want to do CUDA development, so I installed an cuda-compatible NVidia GeForce 8400 card. The 8400 also took over the task of driving my monitor. To use cuda-gdb, the card has to be fully devoted to the debugged task. And the embedded graphics processor on my ancient motherboard won't function if there is a graphics card installed. So I needed something to drive my monitor.

Also I only have one PCI-E slot, which is used by the 8400. So to run my monitor I picked up an GeForce 6200 PCI card.

I was getting strange results. The (lightdm?) login screen looked fine but the gnome desktop showed up at the wrong resolution and I only saw a portion of the desktop. So I decided to replace the driver. I went to Nvidia and downloaded NVIDIA-Linux-x86-304.64.run and did the install process. (Previously I'd been using ...304.43.run, I think.

Now the login looks fine but no desktop comes up. I only see a cursor arrow (at the correct resolution) on a black screen. Did the driver end up on the wrong graphics card? I can't go back and reinstall the 304.43 driver because I can't get into a shell and when I boot it using the recovery option, I'm told there's a problem writing to /tmp.

It sounds to me like perhaps your desktop is being sent to another of your cards rather than the one with the monitor plugged in.
You could try switching to a text terminal and running nvidia-xconfig. This sound give you an xorg.conf which you could then edit if required. I had to use a similar technique when I ran two separate NVIDIA cards.