Hi,
This might help:
Suggested Fan Placement and Cooling
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
Post back with questions/concerns.