I use the bios "smartfan" in the hardware monitor section to calibrate my fan speed. If Q-fan is asus version of smartfan, then I would use it. But if it's windows software, then check the bios for smartfan and try it. I use quiet mode after calibrating; I prefer a quieter pc even if temps are higher.
If you're using Q-Fan and AI Suite together, like with other settings, the BIOS and AI Suite conflict. Personally 'I' don't use or ever install AI Suite, but if you like it then I'm not the one to get advice from on this subject. Further, as I recall AI Suite is required IF you use SSD Caching on the X79.
The amount of BIOS 'control' of Q-Fan (CPU, Chassis Fan(s) 1...3/4/5/etc) depends on your ASUS MOBO and BIOS. The Q-Fan comes with a variety of 'presets' e.g. Standard, Silent, Turbo, or Manual plus fan speed warning 200PRM~600RPM, but again it depends on your ASUS MOBO.
If you list your MOBO I'm fine with looking at your manual. The more advanced will list parameters as I've listed above.
First, the ASUS P6X58D-E has 'okay' Q-Fan control (I have the same MOBO). Next only th CHA_FAN and CPU_FAN can be controlled i.e. the PWR_FAN is 100%; see 2-33.
The ASUS Fan Xpert (part of AI Suite) is probably your 'best' option, but the Q-Fan control in the BIOS works. On the newer MOBO's the BIOS version is indeed improved.
BIOS (see pages 3-28~3-29):
CPU Q-Fan Control -> Enabled ; Disable IF you have a 'pump' i.e. Corsair Hydro series connected
CPU Fan Profile -> Silent ; not the best IF OC'ing the CPU; IF OC use Standard or Turbo
CPU Upper Temperature -> 60C/140F ; try different temperature thresholds.
Chassis Q-Fan Control -> Enabled
Chassis Fan Profile -> Silent
Keep in mind as the load and subsequent temps go up so will the fan speeds.
Finally, test with your typical applications, games, or whatever you use. Yes, you can run Prime95 but remember that's not a 'typical' load. I also recommend using HWMonitor to look at your temps and compare settings (Temp to Noise); link - http://www.cpuid.com/softwares/hwmonitor.html these apps are for testing and don't need to run otherwise.
The 'Defaults' is ASUS Fan Xpert is essentially the same as using the BIOS Q-Fan Control; i.e. the ASUS Fan Xpert offers more customization.
However, since 'I' OC I don't want any BIOS evasive app interfering with my manual OC. AI Suite is always running in the background once installed, like a 'tick'.
This has to do with catch-22's and priorities. For 'me' if the Q-Fan Control is inadequate then my first priority is my OC so I would opt for a dedicated fan controller way before installing the 'free' AI Suite.