I had a CM Elite 120 awhile back with an AMD system. After some experimentation, I settled on having the PSU with fan up pulling in fresh air. It sits too close to the CPU if it is facing down. I too decided that it would cause a lack of air flow over the stock AMD cooler. So I would definitely suggest PSU fan up.
The situation with tall memory sticks will depend on the MB you are using. I don't remember about the little side fan. But I did move the front 120mm fan to the back side of the drive cage to help blow air over the MB and CPU. That little case gets pretty hot inside. I eventually added a 2nd 120mm fan back in the front.