While in the calibration screen, hit the « Enter » key. The calibration screen will toggle between monitors so you can calibrate the extended desktop and have all of the MimioStudio Tools functionality. You can also change the active monitor (usually monitor #1) to the extended desktop monitor.
Note: If using the MimioPad, this only works on the primary monitor. Click here for info on MimioPad on Extended Desktop.
Click here if you run into problems changing the primary monitor.