I have the back and top fans as exhaust while the side fan as intake. I don't put any fans in the front because they are known to vibrate and make a lot of noises. Also if you are going to put a fan on the side panel, make sure to get a dust filter for it because that intake fan will be blowing directly on your mobo and cpu HSF.
Dangle a piece of tissue in front of the fan to verify the air flow direction.
My take is that the front fans should be intake, and they will be filtered.
The top and rear fans should be exhaust.
Air will flow from low cool, front to hot top/rear out.
I would not use the side fan, I think it disrupts the otherwise good flow.
Try it if you have an extra fan as intake, but measure before and after to see which is better.