You might not quite get what I'm trying to say. While the automatic function within ISboxer has changed, I don't see why we couldn't do as I did before, when I was running dual 9800GX2s, only using two monitors (although I had four connected)

I had separate profiles set up for my clients. I would assign two clients to each core of the GX2s, boosting performance.

Ex:

Game 1--->GPU1, Card 1 (This would be my main, only one instance of this profile is launched)
Game 2--->GPU2, Card 1 (Slaves 1 and 2)
Game 3----GPU1, Card 2 (Slaves 3 and 4)
The last GPU core was not used. While I did have four monitors attached, I only really used two. Slaves were tiled and were easily (and quickly) swapped around thanks to innerspace. So I was really split across three GPUs. I'm certain the functionality I'm discussing is still within Innerspace.