You said "unity instances". Did you mean running application instances?
I don't think it's possible to have two Unity windows (I'd like the same thing), but you can make a single window that would encompass the same desktop space, and create separate cameras that would draw in a sub-portion of the window.
For instance, if you have a dual monitor setup, you can make a single Unity window that covers both monitors with a camera that draws on the left side monitor and a camera that draws on the right side monitor. The cameras are independent but part of the same scene.
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