Q: fans running all the time and trouble with displays

Try running Apple Hardware Test on your Mac, http://support.apple.com/kb/HT1509

Actually the first thing to do would be an SMC Reset.

AHT does test sensors (faulty and fans go into over-drive) but not GPUs.

Something you installed.

And while your sig says "10.6.8" that is probably not current.

Monitors, plural, using active dual-link on MiniDisplay Port and one on DVI?

Even RAM can cause trouble.

For a 12-core model if it does run hard all day what are you using to monitor temps and fans? and does it get hot?

Take a look at this link, http://support.apple.com/kb/HT3964

Apple Mini DisplayPort adapters: Frequently asked questions (FAQ)

http://support.apple.com/kb/HT3382

https://support.apple.com/kb/HT3235

Atlona (Dual Link) DVI to Mini DisplayPort Converter for Apple 27-inch LED and 27-inch iMac

http://www.atlona.com/Atlona-Dual-Link-DVI-to-Mini-DisplayPort-Converter-USB-Pow ered.html

CS6 with that much memory you are forcing it to 64-bit mode and all your drivers and plug-ins should be as well.

10.8.3 supports more CUDA capable graphic cards.

The reason for 10.6.8 is to stay with Rosetta.

I would dual boot and put 10.8.3 on its own hard drive - call it testing - and never update over the old, Setup Assistant will bring those apps etc over. You can clone if you want to insure you have more bootable backups too.

Kind of hard not to install anything even if all you do is the software updates offered which can affect other things as well, which security updates have a habit of and breaking something else in the process.

I think everyone should be familiar with all the support articles branching off main support page

http://www.apple.com/support/macpro

https://support.apple.com/kb/index?page=articles