Various panels that comes with add-ons will often stretch in a multi-monitor setup like this. Rather than going into the panel.cfg to manually edit the values, I would recommend using FS Panel studio.
The main reason for this is that the values for height, width, vertical and horizontal positioning of the windows is anything but intuitive. While some of you would appreciate the challenge, I did not have the time to wrap my head around it: FS Panel studio allowed me to accurately re-size and position the panels exactly where I wanted them.
On the other hand: If someone has a logic explanation as to how these values can be adjusted via panel.cfg, I would possibly be intrigued. I had a go a it, but the example given did not make sense.
Resizing of panels and windows for multi-monitor setup:
1. Regular 2D-panels: FS Panel Studio is very useful and handy for this operation
2. ATC-window: Resize the window with the default flight and save it. You ATC windows will now reappear in the same size for all flights.