Hi,
We need the specs of your rig to understand what we are dealing with. Second, I like the Antec Tri cool fans so you can set the speed you need with a little switch, and if you like, you can get them with an LED color light.
Also, please check the bios for temps and voltages so we see a more accurate picture of what is going on in that rig.
General fan placement:
CPU/Heatsink fan blowing down on heatsink
Fan in front of case pulling in cool air
Fan in rear of case pulling hot air out of the case and blowing out the back
Fan on top pulling warm air out of the case (heat rises)
Most instances, side case fans pulling cool air into the case with the exception of any very near the top of the case to take advantage of the hot air rises scenario.
Smooth air flow front to back in case
Other Considerations:
Move ribbon cables out of the air flow area if possible
Suggest round IDE cables for best air flow
If your temps are real high, you might want to redo the thermal paste.
Post back with questions/concerns.