If you somehow manage to have a choice (but its not obvious how to do this from the installation link from thermalright), then why not try both orientations, and use some CPU Temp monitoring software to see which works best.
I actually ended up pointing the fan up. I used artic compound on the unit. I first used my finger to apply it because no instructions came with the compound, and I just didn't know. Then I found this http://www.arcticsilver.com/ins_route_step2intelcmq.htm... after the fact, so I used Artic's cleaning kit to take the compound back off and then reapply it. Thankfully the system was never fired up before I caught the error about my finger. As to how much to apply...I really didn't have much of a choice. They make it look easy in the picture, but the stuff goes on like cake. I now have a pretty thick layer of this crap on, and I couldn't do much about it. I haven't gotten to loading the OS yet because I am having floppy problems and I can't load the RAID drivers yet. I am trying to find a work around, then when I get into the OS, I will start checking out temps. and report back.