STO should and does utilise both GPU's at least on my 4870x2 under XP and Win7
ive played arround with rivia tuner and checked over time that both GPU's are being used but if you run STO in a window or fullscreen window then SLI does not work you need to makesure STO is running full screen
under video troubleshooting makesure multicore rendering is still switched on, it should be on by default
An ATI profile is not going to help because the game has to be coded to use dual/multiple GPUs. This is why buying SLI, Crossfire, or GTX295 ATI5970 is not always worth it.
It does use dual GPu's and even tri-gpu's. It's a fault in the driver for the latest GPU hardware. ATI and Nvidia have already acknowledged this, and ae ushign out driver updates and hotfixes faster than ever before to fix it.