PSU intake downward is better. PSU needs more air space for exhaust rather than intake and downward exhaust also makes the bottom intake less effective.
I did a test on my 500R which has the exact case fan placing(except that the sides directly blow air into the GPU) and I found, the 2nd top mounted fan would be better served as an intake since it increases the intake of my Hyper 212 EVO making better CPU temps.
The PSU fan is an intake fan. So if the fan is facing the bottom vent that counts as an intake. That way it doesn't use the air inside the chassis. Its its own sealed unit.
What I've been reading a positive air pressure is better than negative. That is more air being pumped into the case than being exhausted out. I do know that it helps keep dust out, I'm not sure how it helps cooling but apparently thats what it does. I got that from recent reviews on anandtech where reviewers were saying positive is better.
Your case has 3 exhausts and 2 intakes. Are your sure that the case has fans on the sides for hdd cooling and not just vents? 2 extra intake fans for the hard drive cooling seems excessive. I would remove one of the exhausts on the top.
Sorry I thought the PSU was exhaust. But it's intake. So the PSU intake is facing the bottom. The reason why I have an intake on the bottom ( not the PSU intake ) is because it blows air directly on my GPU. I don't actually have any HDD in the bay I just thought that if the fans on the sides are exhaust that it would suck some of the airflow from the front intake, rather then push the air towards the MOBO, GPU, CPU
"Are your sure that the case has fans on the sides for hdd cooling and not just vents"
Positive. The case came with the fans sitting on both sides. My theory is that the 2 fans on the sides are small so they produce a very weak airflow. And since the fan on the front is much bigger that it would push the airflow from the HDD fans towards the motherboard since it is a bigger fan and the airflow would be much more powerful.