You can, but unless your processor has hyper threading, it isn't going to help performance at all. And yes, they do work on separate work units. Some people run several installations so that it can download several work units while connected to the net, then they can have it fold for a week with out needing to download another unit (unconnected to the net. You can just do several installations of JUST the console version or JUST the graphical version. Just install them all into different directories (FAH1, FAH2, FAH3), and give each installation a different machineID.
But again, if you don't have hyper threading on your CPU and you don't have to worry about the computer not having internet for awhile, I think it hurts performance.