I assume that you're trying to find the best clocks for your SLI setup. I ran into the same problem when trying to test for artifacts with ATI Tool in that I wasn't every able to get it to use the second gpu. I think it has something to do with the fact that ATI Tool runs in windowed mode only. Although, this might have been addressed with multi-monitor support in subsequent drivers.
Anyway, I ended up just finding the best clocks for the card individually, and clocked the pair at the lowest common denominator. This seemed to be the easiest, quickest way to accomplish what I was trying to do. If you're just trying to stress test the cards for heat/reliability purposes, just loop 3DMark or Crysis benchmarks for a while.