Re: Applications for settings (and saving) Monitor(s) Setup
When I plugged in my external monitor, I went to Preferences> Monitors, and set them (both, as it is best to have similar resolutions on both to make the screen heights match) up as best I could and then clicked on make default. This did not override my single monitor set up (1280x800), but does automatically adjust them when the external monitor is plugged in (both set to 1280x720, my external does not support 1280x800).
Dell Inspiron 1501 AMD Sempron, 4GB RAM, 320GB HDD, running 12.04 64Bit
Justop Media Centre with Lubuntu 12.04, and Android
Raspberry Pi running Openelec XBMC
Ubuntu User #32384