My main advice for anyone doing something like this is to ensure that the "hot" side of the heat pipe is below the "cold" side where the cooling fan is.
Putting it upside down means the heat pipe has to work against gravity and that's bad.
Even along the same plane isn't great, then it has the wick back the condensed cooling fluid, which is less efficient than simple gravity transfer back down.
Huh, I always thought the heat pipes are just plain copper (or similar heat-conducting material), never crossed my mind that there could be a cooling fluid inside.
They generally have a wicking material in there to handle the pipe being in a poor orientation. They would be MUCH less effective trying to just conduct heat to the cooling fins.
Putting it upside down means the heat pipe has to work against gravity and that's bad.
Even along the same plane isn't great, then it has the wick back the condensed cooling fluid, which is less efficient than simple gravity transfer back down.