The stable version of AtiTool only detects 1 of the video cards, and the beta version, detects both, but doesn't actually change the speed.
I have not yet sucessfully tried Rivatuner yet. I'm confused about that preference of protecting a certain area of memory or something, and I don't want to use it until I read more about that.
I will look into NiBiTor and nvFlash.
As for why I want to.
Well my 8800 GT cards are factory overclocked to 625mhz. I was playing Crysis, on high settings, but I started seeing blocky blurry pixels. I'm pretty sure the cards are getting too hot.
I bought a bigger fan and a second fan to ad to my case. In the mean time though, I'm trying to keep them cooler by underclocking them back to the stock 600mhz that they normally are.