PCI refers to the, normally, white slots.
Usually AGP are brown. Newer motherboards have PCI-express which seem to vary in colors (just from the ones i've seen).
yes, you can run one monitor off of each of two separate PCI video cards (or just buy one card with two VGA outputs). I've only tried it in linux, and I was able to set it up as one massive desktop, or change it to two distinct desktops. I imagine windows is the same way.
It may depend on the drivers for the cards, but I had a friend who ran 3 monitors with no problem (one dual head card, and one single head). he ran them as three individual desktops, IIRC.
eta: be aware that you may need a pretty good power supply to run that much hardware.
