I've added an experimental window positioning preferences mechanism to MASON. Still not sure how to place the GUI buttons for this, and it's fairly flickery (which I might not be able to get around due to when people normally programmatically set their window locations).
In short, you can now take all your displays, move them and size them as you like (and hide or show them as you like), then in the Displays tab you can press "Save" and save all these values. When you load next time, the windows will try to come up like that.
Rather than impose a unique key on each display, MASON's relying on the window order being consistent. So if you programmatically change what displays you're adding and recompile, funky thing might happen (just press "Reset" to delete the preferences and you'll be fine, then quit, reload, and press "Save" again when you have it set up).
It's out on SVN. Let me know what you think.