I run dual screen as well and play in windowed mode too. What i do is i use an app called Ultramon. This offers lots of features to those of us with dual screen setups but the one of importance here is it allows you to lock the mouse to the active screen. You can map the command for thet to a hot key, so when you fire up DG hit your hotkeys and the mouse stays on the main screen just like the 2nd monitor was never there.
Personlly i dont use it for DG, i use awsd for movment controll in game and just don't seem to have issue with the mouse. I also don't get any crashes from moving from one screen to another in game either, so it has been less of an issue for me.
Search for it mate..it's a great little app and not very intrusive.