According to Dan Vrátil and Alex Fiestas, KDE will have an advanced multi-monitor handling that should works without too much intervention. They are now working to collect all possibilities that could happened with multi-monitor environments.
The promising tool will land in KDE soon and if it's implemented, it will have the similar experience like in Windows environments (and probably even less complicated). In short, it will make working with multi-monitor so much easier.
Here's a video showing the current work