Here's my setup:
2 monitors at my desk set up as 1 screen using twinview
1 monitor(tv) set up away from my desk as a seperate x screen.
When I have all three screens enabled, the two monitors at my desk no longer act as separate monitors.
In two screen mode, I can maximize a window on one monitor, and it will only maximize on that monitor. Also AWN and any screen that pops up in the middle of the screen opens in the middle of one monitor.
In three screen mode, when I maximize a window, it maximizes across both screens, filling my entire desktop. The monitors no longer act as separate monitors.
For example, if you look at xorg2screens.png, you will see that the firefox window is maximized and I'm going to load up the GUI for yum. It's cut off in the middle of the screen (where my two screens separate.) If you look at xorg3screens.png, you will see that the maximized window takes up the whole desktop (both screens) and the loading screen for the package manager loads in the middle (right where my two screens meet).
As hopefully you can see, this is very annoying. I have attached the two xorg.configs I was using for each setup. Maybe someone can point out where I'm going wrong?
I hope the attachments work. If not, I'll try to post them somewhere else.