I'm thinking #1, because blowholes are designed to exhaust heat up and out of the case. But do us all a favor and do both, measuring your temps (CPU, video card(s), mobo, etc), and find out which one is actually more effective.
Ok, having used the Extreme in a TJ09, let me tell you, they dont get hot. The pipes didnt even get hot running passively. However, hot air rises, so I recommend #1 all the way. The 8800's get really hot so having the roof fans suck up and out, is the best route.