This is an extremely annoying bug. As others have mentioned you can set
apps to open on on a different monitor. I open all apps on my primary
monitor. See
http://ubuntuforums.org/showpost.php?s=6c9b13a5e06988d3413925dd3937ce60&p=11852920&postcount=3

You can also drag windows with Workspace switcher. Simply click to show
all workspaces and drag windows to appropriate monitor.

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https://bugs.launchpad.net/bugs/754508

Title:
  Modal dialogs don't appear on the same workspace/monitor as their
  parent window

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