You will sometimes hear it kick up on it's own. The HDD fan is fine left on auto, and the system fan is for the liquid cooling unit. The lower you keep your temps the longer your gpu will last. They put it there for us to use, because heat is the enemy. It retails for around $125, when other 92mm fans on the market are cheap $10 fans. The PCI fan in your rig is actually a high output(an AMAZING 110 cubic feet/minute) heavy duty server fan. It works really well, but auto just doesn't cut it. These rigs are designed for the PCI fan to feed fresh air to the gpu and for the gpu to pull that air through and out the back. And always use your manual fan settings in your Catalyst Control Center for your GPU's.

I just go bump it up before I start my game, and set it back to auto when the gaming session is over. Watch your peak gpu temps, if they get higher than you want then use a higher manual PCI fan setting in the Alienware Command Center. Learn to use it in concert with the manual fan speed adjustments in the control center. Real Temp is a must have as I like to know what all my (specific)temps are at all times. Of coarse you know that the temps you see in the Alienware Command Center are ambient temps, not cpu temps.

And because it is really small and lightweight you can run it as long as your pc is on, through gaming and everything else. It also has an alarm where you can set the peak temperature that you're comfortable with on your cpu and gpu, and it will go off if your rig crosses that threshold. It even shows what your peak temps were and when they peaked. It is a really lightweight program that really does not use any resources which gives you cpu load, cpu temps and gpu temps in real time. You should start by downloading Real Temp GT 3.60.

Alienware command center fan control