From my experience, the GTX 2x0 series cards based on the reference design had the fan working as an exhaust, with the whole GPU shroud channeling air from the fan out the back of the case. The reference for the 460s is a standard fan, that blows the air around everywhere. I prefer the exhaust method, and I bought the EVGA 460s with the external exhaust fan.

I'd check out MSI Afterburner. It's an overclocking utility, but you can also control the fan with it.