The reason you want to blow the air upwards is that you want to evenly distribute warmed air over a higher volume of space.. so the air that will be moving downards will be moving over the heating element into the incubator. It also allows some air to be vented out of the incubator and fresh air to be sucked in from the bottom vent holes. With the fan blowing down, the warmed air is sucked in from the heating elements and blown directly down on the eggs some being directly inline of the fans exaust. Also it will blow directly on your water so the humidity will go up. More air is sucked in from the upper vent holes due to their size and closeness to the input of the fan.
It would be easier to see a drawing of the air circulation I'll see if I can find one.