TL;DR: I’m aware of the window placement issues and I’m working on it. A fix should be coming within the next week.
A lot of the issues here are related to the initial placement of new windows on the screen. I’m working on getting the mechanism right so that most windows and dialogs will remember their previous location and if they have no remember previous location will appear in a reasonable new location on the overlay ‘desktop’. Once it’s done it should be a global fix for all the windows that currently appear with their frame partially obscured in the upper left hand corner.
This global work will also include ensuring that all open elements remain on screen even if the overlay changes resolution or shape.
In the long run I’d like to be able to support either overlay or desktop windows for most of the elements. If you’re editing your domain in 2D mode and you want to drag windows to another monitor you should be able to. The problem here is that while that probably wouldn’t be too hard to support, getting windows to switch from being in the overlay to being on the desktop (or vice versa) when you switch display modes is likely to be tricky.
However, the first step is making sure everything that’s needed can be rendered in the overlay, and once that’s done I can tackle more ambitious ideas like this dual-mode thing.