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I am trying to setup Rift to run with 2 monitors, I have used the wizard to set it up with default settings. Unfortunately it seems to be configured a bit ackward for me. It splits up the game windows across the 2 monitors just fine, however when I click the game window on the 2nd monitor, the window switch from one monitor to the other. What I would like it to do instead is stay on the 2nd monitor and allow me to input to that window like normal when selected. I try turn switching off on the regions, but that only seem to make both windows stay on the 1st monitor.

You want Focus Follows Mouse. That is often paired with Per-window Hotkeys.

Thank you, that was exactly what I wanted.