So, what are the max temperatures the CPU is hitting?
And what is the GPU? Depending on the cooling system, it could just be blowing some of the air into the case.
On the positioning, I would have thought an horizontal airflow would be the best option so it draws less from the GPU and ejects it straight out of the back rather than making the PSU slightly warmer.
Not much experience with side panel fans on how it affects the airflow...I think if the rear exhaust feels warm, the side fan would help getting rid of the heat inside the case. I only remember this from my brother in law's PC, which I could feel the heat being exhausted at the front really warm. He had to buy a side fan and possibly (I don't remember) cut a hole through the case.