Probably would help if you provide more info on your video card(s) and what video driver/software you have installed.
I run dual monitors by having an AGP card and a PCI card installed in my computer. Both cards have nVidia GPU chips. Thus, they use the same driver. I have nVidia nView Desktop Manager software installed. I can have two different desktop backgrounds.
If you have a similar hardware and software configuration, I may be able to help you. If you're using an ATI card, I don't think I can help.