i know no way of turning just one monitor off without affecting the desktop layout, as with xrandr, the desktop is really just one big screen. if you could turn one monitor off, some output might still be used on that part of the desktop that is in the power down monitor, creating hidden content. But with the increase of multihead setups, this might be a good time to revive the X11 bug about this: X11 bug #1658
I personally use the "KISS method": i press the monitor power button when i don't need it, and press it back when i do.