I am with Ubuntu 13.04 and currently using two monitors. My Compiz Settings are by default
General Options -> Desktop Size : Horizontal Virtual Size = 4; Vertical Virtual Size = 1; Number of Desktops = 1 Desktop Cube -> Multi Output Mode: Automatic
What happens now: I can place applications on both of monitors. When rotating I have the cube and the cube faces are as follows: [monitor1][monitor2][monitor1][monitor2]. But When I rotate the cube and if I am on monitor1 I am not able to switch to workspace from monitor2. I see it but when I end rotating it just rotates once more to the nearest workspace form monitor1.
The reason for this is that sometimes I get the second monitor turned off and I still need to access the applications on it