In regards to side fans:
In my experience, they always work best when turned down to low speeds/low CFM. If they are too high, they will either suck out too much air and the video cards will be able to pass enough air to the back of the CPU to keep it cool, or they will push more air than the video cards will suck through and start sending hot air from the GPU up to the CPU.
I prefer pushing air in than pulling it out, because if the fan is right next to the GPU, then it needs to be making the job of the GPU cooler easier by giving some pre existing airflow to suck through to the back. While pulling it out will most likely see a better result in ambient case temps, it will make it harder for the GPU coolers to get the air it needs and raise the GPU temps, which are usually closer to max temps than the MOBO.