Heh, good question.
It's a little argumentable but some say that having the fan blow down toward the heatsink will perform better. I also have an alpha PAL35 with the fastest 60mm fan I could find. (6800rpms!!) I have it blowing upwards, but I think Iam going to do some test in the near future to confirm which way is better.
About which way it blows, if its a 3 prong connector, simply plug it into the motherboard, start it up for a second and feel with your hand. If its a 4 prong connector, plug it into a power supply cable, unplug the motherboard power cable, and again feel with your hand which way it blows.
Pretty much, you can't go wrong.