Hello, from my understanding, the bitcoin miners will allocate 1 core for each GPU
would A) with 3 Radeon 6990's attached to the system, only 3 cores of my quad-core CPU will be used
would B) with 3 Radeon 6990's attached to the system, it would be preferable to have 6 cores as all of my cores would be used
What if I had two CPU's on this motherboard

I can use a 1600W power supply, but I fear this may be oversaturated too (but I'm open to underclocking the CPUs)
For the most part if you have a dedicated mining machine under Linux you don't need to worry about the number of cores. The CPU is engaged only for brief periods. I have a 6990 running on my 12 Core box and each instance is using < 1% CPU. Under poclbm use the "-f 0" flag.
I have my 6990 clocked @ 980/1260 and the whole rig (including two hex-core Xeons, a GTX480 running at full load and ten SATA drives) uses 850W - as measured from a watt-meter which is constantly attached. Given that my 6990 runs around 350W a 1600W PSU will probably be fine. You probably won't be hitting peak efficiency as most PSU's are designed to get the maximal efficiency (80%, 85%, 92%, etc) at the middle of their available load. Also I tend to find that 120V PSU's > 1200 tend not to be designed for the higher efficiency specs. 220V PSU's however are more efficient - ie it's much easier to find 90% efficient 220V PSU's (and single voltage PSU's even more so but I'm getting off topic).
Jono