The side fan is to cool the GPU's more (graphics card) So intake will give them more cool air, and exhaust will take more hot air out the case. Dependant on the average temp inside the case determines what you do with that fan. If the case inside is warm, you want more exhaust fans. Generally you want the CFM (cubic feet per minute) to be roughly the same in and out. So if you have the specs of each fan, work it out as simple maths

. Or you could simply put it in one way, do a benchmark and watch the temps, then do it the other way and use whats best.