It seems like the best design would blow air out away from the heatsink, and the cooler air would get sucked back through right?
I've seen both designs. Personally all HSFs I've used have blown air out from the heatsink and I think that's more common, but it's really not a big deal. As an engineer I can sort of explain the argument behind each design:
<font color=orange>Blowing air *out of* heatsink</font color=orange>
Produces a smoother and more "laminar" flow than the other design because you're blowing straight out into open air (nothing in the way to disrupt the flow). Hence less pressure drop through system. Hence greater velocity and volumetric flow of air over heatsink fins. Hence faster removal of heat.
<font color=orange>Blowing air *onto* heatsink</font color=orange>
Produces more "turbulent" flow because the heatsink is sitting right in the way which disrupts the flow. More pressure drop and hence lower velocity, BUT turbulence improves heat transfer. Also, this design will probably cause the moving air to touch more of the heatsink (and hence remove more heat), due to the chaos and turbulence. The other design is more likely to find "pathways" through the heatsink that present the least resistance, which may cause parts of the heatsink to have hardly any air flowing over them.
The pros and cons of each design probably roughly balance out and in the end it doesn't make much of a difference.
If I switched red & black, would that reverse the fan direction?
Maybe, depends on the motor. Some motors can be reversed by switching the current around, others can't.
Anyway, run Toast for ten minutes and if you don't lock up you're fine. Instabilities generally arise with CPU temps around 60°C, but I would never trust the CPU temp reading on an Athlon system since the vast majority of Athlon mobos don't use the core diode for temps. They use an inaccurate reading off the socket, which can easily be 20°C or more off the core reading when temps are rising rapidly like in Toast. So the only true guage of your CPU temp is whether or not you're locking up.
Ritesh