Full screen zoom: follow keyboard focus doesn't work well
I can't help you with Word, etc., but here's how to get it to stop recognizing the Cintiq:


Go to System Preferences.
Open the Displays pane.
Click "Detect Displays."


If the Cintiq is turned off, this should fix it. When you want to re-detect it, simply turn it on and Detect Displays again.

If you want a quick way to access Detect Displays, there's a menu bar icon that can be enabled for Displays tools while you're in the same preference pane: Tick "Show displays in menu bar" and you can have quick access to that as well as a few other relevant things.