My dad used to run a Nvidia 6800, and when he had both monitors hooked up, there would be a performance hit. For him, he had a HUGE performance hit. untill he went into the bios and noticed that the defult Display adaptor was set to PCI. Once he changed it to AGP, That fixed alot of his problems.
After that, the performance hit was ALOT lower. But there was still one. i can't tell you how many FPS's he lost. and he got that hit from usually playing Guildwars, or City of heroe's, and his 2nd monitor usually running firefox so he can browse his guild's Forums.