heat transfer (HT) is drastically improved when the fan is blowing onto the heatsink. HT is directly proportional to the fluid velocity (in your case air) passing over the surface of interest. if the air is being sucked from the sides of the heatsink and out of the fan, the fluid is probably in laminar or transition flow. if the air is being blown down onto the heatsink, it is probably in turbulent flow. Turbulent flow is capable of moving far (more than 2x) heat than laminar and transition flow.
the only negative that i can forsee when blowing down onto the heatsink is the mobo will be in more direct contact with the hot fluid coming off the CPU and possibly raise the temp of the area around the CPU. If your case is respirating reasonably well, however, you will not need to worry about this. (good respiration: make sure you have air INTO and OUT OF your case)