And finally before we move on to the instructions, it will benefit you to understand that using multiple video cards is not the same as multiple CPUs. It is a common misconception that "GPU Affinity" can be configured similar to "CPU Affinity." This is not the case. Direct3D windows are tied to a monitor, not to a GPU. This unfortunately means that you cannot have a window rendered by a GPU that is not powering a monitor. As of ISBoxer 38, ISBoxer automatically selects the monitor for your game instances, based on your Window Layout.
Lax, that is perfect - the exact information I needed.

Each GPU will process for it's own screen and not the other - this means it is worth having my old vcard in the machine alongside the new one.

Note one's ATI and one's Nvidia - i couldn't possibly SLI them anyway.