Using the information found here I was able to stick one GPU into auto fan mode, however the second GPU would stay at a fixed value and be overheating.

Looking at the man page for nvclock I found that you can use a command line switch to list and control individual  GPUs.

First install nvclock and nvclock-gtk

sudo apt-get install nvclock nvclock-gtk

Secondly open up nvclock-gtk

sudo nvclock_gtk

You may need to set a fan speed under ‘Hardware Monitor’ for each GPU, after you’ve done this use the following commands

nvclock -s

This command gives a list of all the (nvidia) GPUs connected to the system.

nvclock -c 1 -f -F auto

nvclock -c 2 -f -F auto

Repeat the above command for each GPU you want to be put in auto mode. You should now see in nvclock-gtk the fan speeds, under ‘Hardware Monitoring’ adjusting up and down, automatically on there own.

If you want this done automatically at login then you can add the commands (one at a time unfortunately, unless you make a script) to your sessions System > Preferences > Startup Application as shown here