Well I just got done (yesterday) with my case mod, I will post pics when I can get my camera to work right, but what I did was this.
I cut out a 92mm hole in the front bezel, and the front chassis, and mounted a 92mm w/ air filter. I cut out the 80mm hole in the back of the chassis where my 80mm exaust fan is mounted. And I cut a 120mm hole in the top of the case and mounted a 120mm fan. I also have an air vent in the front, top of the case to prevent a vacum condition.
I really wish I could say that it made a great difference in my temps as I had hoped but nothing more than a 3C drop in my case temp and 1C drop in CPU. But I really don't think that the temps are reported correctly. I think I may have reached the limit in what I can do with air cooling.
As far as a side panel fans, i would say go with intake, and check your temps. write them down after 10 mins. Then change 1 to exaust and check the temps after 10 mins. Then set them both to exaust and check the temps after 10 mins.
I really don't think that setting 1 to intake and 1 to exaust will help at all if there are less than 4 inches apart, as you would only be circulating the air the blowing depth of the fans, but with that said you will most likely be blowing enough air with 92mm fans to hit the motherboard and components. So it is a toss up, really.