When I go to the Activities-corner, all my windows from all my desktops becomes visible kind of like the scale plug-in works. However, I have many windows and I have my desktop well arranged and want only the windows from my currently active desktop to show up. How can I achieve this? I'm not afraid of hacking a bit, but I don't know where to start. :)
Are you sure it isn't the known bug #844881.
When you go to Activities or press the [Windows]-button only applications from the current workspace should be visible. If some windows are displayed overlayed you are a victim of the obove described bug.
The only thing you can do then is press [Alt]+[F2] and type in