For years, I had trouble with what was once separately managed as Spaces and now is an incorporated part of Mission Control. I use two displays on my Mac mini, and at some point, something broke. Yes, I could do a clean OS X installation, but we all know what a pain that is in restoring yourself back to where you were. (And see my horrible, no-good, very-bad time earlier this month with broken drives and a failing older Mac.)
I wanted to use the option in the Mission Control preference pane labeled Displays Have Separate Spaces. I always want certain apps in my smaller, right-hand display, which is off to the side, and other apps always in the main 16:9-proportioned newer, central monitor. In some cases, such as my email software, I want the window in the right-hand screen, but new messages to appear on the main screen, which also contains the default system menu bar and drives.