CS6 uses the boot disk for scratch and can put 100's of GB on there if there is room, and can cause trouble and overload the SSD.
So yes you need to find another location for scratch.
PCIe lets you leave your drive bays as they are and allow you to add two SSDs that will run faster and not impact performance.
I would aim for keeping the boot drive to 60GB free.
I would also want to see the 500GB drive upgraded to 1TB or larger (use the 500GB for backup clone of the system for one thing).
Your 2TB is where I like to see: 50% free area.
You need to make a backup system image of the SSD with CCC and then restore from and booted from the clone and restore back to the SSD at some point soon. Use this SSD for scratch or another seeing you have a free hard drive bay #4 still open until you can get a PCIe Sonnet card (US$150-300).
Install TRIM Enabler 3.0 now and use Onyx after that.
There are more options today but the basic ideas, from MPG:
http://macperformanceguide.com/OptimizingPhotoshop-Intro.html
http://macperformanceguide.com/OptimizingPhotoshopCS5-Benchmarks.html
MPG LLoyd's site, is a graphic photographer and edit.
Eventuially a newer even a 2009 Mac Pro and better GPU and more cheaper RAM would make sense if you want to as would 10.8.5.
Or save up for Mac Pro 6,1 or to buy a used Mac Pro 2012 even. Some things you can take with you and re-use.
Look at your 8800GT.
It has one power cable. There are two thumb screws holding a bracket bar in place. So you can remove or upgrade or clean.
Small, 512MB VRAM, can run hot, can get dust clogged inside and need to be cleaned out. And could fail from heat and weak solder joints (take apart, bake in oven for 15 minutes at 350*F actually works, is documented how to do on Youtube). 10.6.8 does not provide as many options in graphic cards.
It seems like upgrade to 10.8.5 $19 might be worthwhile some point (another reason to 'clone' your system or start fresh with a new SSD for system, so you can if needed continue to boot and run 10.6.8).