if you set the monitors up using the extended desktop feature in windows then yes you can have a program on each screen. Eyefinity is where you use CCC to make the multipule monitors act as one large monitor. And crossfire is certainly compatible, allthough does give you more outputs. You have to use the outputs from the card in the main PCI-E slot, so to use 6 monitors you would have to get an eyefinity 6 gfx card, not have 2 eyefinity 3 gfx card, if that makes sense.
1.When Eyefinity isn't running a game on 3/4/5/6 monitors, will you be able to use the 3 monitors separately? Like one with photoshop, one with firefox and one with MSN?
If you disable eyefinity in CCC and put each monitor as extended desktop in windows, yes you should. If you maximize a window, it will fill up one monitor.
If you keep Eyefinity, you have to adjust the window size of each application and position them carefully to match each monitor. If you maximize one window, it will spread out to the three monitors as if its one big window.