its best to have the air comming in the front, and exiting the back, and a side fan blowing on the motherboard is probley good too, you want to mantain positive pressure in the case by having more input fans than output fans, then you can have filters on the intake fans and very little dust will get in, with negitive pressure, dusty air gets sucked in though all the small cracks in the case,
in my computer i have a 120mm fan in the front, 120mm fan in the back, and a 90mm fan in the side, i have the front air intake filtered, and the side will be when i find a good filter.
also, most cpu coolers blow downwards, so if that side case fan is blowing out, it could be making both fans work harder and cool less, i think the best way is to have the side fan blowing in, so it blows air into the cpu fan, but this only works if both are going the same direction.....