Removing heat from the case by means of convection alone is marginally effective, depending upon case design. Forced air is almost always required in today's computers, so without an exaust fan, your CPU cooler fan must run higher RPM to adequately cool the CPU with recirculated warm air. Adding a 3 wire exaust fan and plugging it into the motherboard may allow you to contol both fans. Since the CPU will run cooler, you may be able to reduce the RPM on both, and thereby reduce the overall noise level.
Hope this helps. Enjoy!