In this hobby, It's a matter of what makes you happy.
B&W 804s are very fine speakers. The fact that they're full range doesn't diminish their ability to play classical and jazz music very well, and with the wealth of great Multi-channel classical and jazz SACDs available, you may find that your using the multi-channel rig a lot for pure music listening. To improve on the 804s, you'll need to be prepared to spend a good chunk of change on a pair of monitors, but there are many out there that would fill the bill.
Yes ,you'll have to power them with something, so a pair of monoblocks would be in order. As the 990 has both balanced and unbalanced outputs, feeding the additional amps wouldn't be a problem. You could set the second 12v trigger to turn one amp, or set of amps, on or off dependong on the input being used, but so far as I know, the second amp, or set of amps, would have to be turned on or off manually.
A lot of folks have seperate hometheater and 2 channel listening areas. I dont think I've ever seen multi-channel and seperate 2 channel set-up in the same system, but I can't hink of any reason why it shouldn't work well.