I've gone through more times than what I would like to admit. It really depends on the heatsink, the path of airflow in your case, and the amount of heat generated by the fan's motor (they get hot too).
In all cases, I'd advise you try both ways to see which works best for you, regardless of what the heatsink/fan's manufacturer originally intended. Yes, it's a bitch and it's a lot of work, but it's the only way. I do have to say that if you try it with the fan pulling air away from the heatsink, you MUST use a heatsink shroud in order to gain the maximum amount of benefit from it. For heatsinks that don't normally come with a shroud, you an easily fashion yourself by wrapping a strip of aluminum foil around the top of the heatsink (ala PAL series).