I have a MacBook Pro (OS X 10.11) with one HDMI monitor and one USB monitor. The MBP is on the left, HDMI in the middle, and the USB is on the right. Each monitor has ~3 workspaces (meaning I usually have a total of 9 workspaces).
My overall setup seems chaos with regard to on which monitor, and in which workspace, apps launch into. I launch apps via the Dock and Finder.
Example: On the USB monitor in workspace #8, I double clicked a .docx file in Finder. At the time, I had workspace #1 displayed on the MBP. The MBP monitor all the sudden flipped to workspace #2 and opened the document.
Likewise, launching apps from the Dock gives inconsistent results.
Note: The behavior that is most logical does happen when you start Launch Pad and System Preferences from the Dock.
- put mouse focus in the monitor and workspace you want.
- click on the Dock for Launch Pad or System Preferences.
- they launch in the monitor and workspace that has the current focus.
For apps like Chrome, Excel, NetBeans, iTunes, etc. that does not happen. I can't figure-out how OS X decides which workspace to put it in.