Depends on where your power supply is. If it's above the cooler, then have the fan blowing up so the hot air can be exhausted through the power supply.
I wouldn't think it would be that safe to do it that way, would it?
You have to look at the blades to see which way the air is blowing. The air should be blowing INTO the heatsink.
That's not what I mean...it is blowing into it. (but you can go both ways)
I think I'll point it up to suck air off the GPU and keep the general airflow of the case constant.