OK...
In general, cool air in from bottom front, hot air out top rear. Have the fans orientated that way. Most often, intake fans are not needed. Exhaust fan(s) remove air from the case and it has to be replaced. Intake will take care of itself.
The problem with the ATX design is it has no dedicated heat paths. The case is just one big box with heat circulating round and round. People often add WAY too much cooling by adding a bunch of fans which moves more air than needed and just adds to the noise problem. The BTX design will have a thermal zone for the CPU that will intake air from the front of the case, pass it over the CPU and send it out the back instead of just blowing it around the case.
I run a very quiet rig by doing things a little differently. No need or tons of noisy fans. For my CPU, I use an 80mm Panaflo M1A which runs ~ 2400 RPM @ full speed, 28 dB. The speed of that fan is automatically varied based on CPU temp using a utility called
Speedfan During low load/temps, the fan runs @ 60% RPM. When the CPU/load goes up, speed increases.
Instead of using the hot air from the case, I use a duct than runs from the CPU to the front lower intake of my case. This provides cool outside air for the CPU and doubles as and intake fan.
CPU ducting kit. The Power supply above the CPU (Antec True330) which also uses variable speed fans and a Panaflo L1A case fan (1900 RPM 21 dB) @ full speed exhausts the hot air from the CPU. The L1A is also controlled by Speedfan. It runs 60% RPM until temps rise, then it goes to full RPM.
For video card cooling, I use an
Arctic Cooling Silencer. Again, instead of circulating hot air around, it exhausts GPU heat directly out of the case. It cools better and is quieter than stock and also doubles as an exhaust fan.
With some thought, you can have a very cool running, stable, and very quiet system, and it doesn't cost a ton of $$ either. This setup cools an overclocked system of a P4 2.6C @ 3.34 Ghz and a Radeon 9800 Pro.