Use the fact that heat rises to your advantage.
Identify components that will generate heat. (MB, PSU, monitor, etc.)
Fan(s) above the heat source should usually blow out.
Fan(s) at the heat source can go either way, depending on the desired air flow path.
Fan(s) below the heat source should usually blow in.
Position fans so that the exhaust does not loop back around to the intake due to:
1. The angled back of your build being placed near a wall/obstruction that traps/reflects a downward angled exhaust fan
or 2. The intake and exhaust being too close to each other
Don't make a cooling system
pushmi-pullyu -- balance your intakes and exhausts.
Scott