First thing to start with is to run the coolbits tweak to allow setting of the card fan controls.
sudo nvidia-xconfig --thermal-configuration-check --cool-bits=28 --enable-all-gpus
Just run this in Terminal and reboot. This will write a new xorg.conf file that set the the coolbits for each gpu. Then if you pull up the nvidia-xserver settings app, (you should just dock this to the Launcher permanently for easy access) you pull up the Thermal Setting for each card, select the checkbox for fan control and slide the fans speed slider to what you desire. You can also use the Power Miser settings to apply the overclock you want for core and memory transport speeds. You will be running in P2 state for each card as Nvidia's driver automatically hamstring the card when they detect a compute load being run. By overclocking the card in P2 state, you can get back some of the clocks the card would be running in P0 state if Nvidia didn't downclock them. Just be cautious and sensible with the overclock.
OK, I got this error when I ran the first time, then as you can see I ran it again:
mark@mark-TR5-linux:~$ sudo nvidia-xconfig --thermal-configuration-check --cool-bits=28 --enable-all-gpus
[sudo] password for mark:
Using X configuration file: "/etc/X11/xorg.conf".
VALIDATION ERROR: Data incomplete in file /etc/X11/xorg.conf.
At least one Device section is required.
Package xorg-server was not found in the pkg-config search path.
Perhaps you should add the directory containing `xorg-server.pc'
to the PKG_CONFIG_PATH environment variable
No package 'xorg-server' found
Option "ThermalConfigurationCheck" "True" added to Screen "Screen0".
Backed up file '/etc/X11/xorg.conf' as '/etc/X11/xorg.conf.nvidia-xconfig-original'
Backed up file '/etc/X11/xorg.conf' as '/etc/X11/xorg.conf.backup'
New X configuration file written to '/etc/X11/xorg.conf'
mark@mark-TR5-linux:~$ sudo nvidia-xconfig --thermal-configuration-check --cool-bits=28 --enable-all-gpus
Using X configuration file: "/etc/X11/xorg.conf".
Option "ThermalConfigurationCheck" "True" added to Screen "Screen0".
Backed up file '/etc/X11/xorg.conf' as '/etc/X11/xorg.conf.backup'
New X configuration file written to '/etc/X11/xorg.conf'
How do I run the "nvidia-xserver settings app" ??