@YannBoy: unfortunately, I didn't find any solution for now.
I kind of put this on hold but I think I'll have to write myself a little app to do the trick since I couldn't find anything existing.
@hang-the-9: well, I as tried to explain in my first post, I don't see the second screen so when I'm moving a window from one screen to the other, I don't know where it is on the second screen.
Thanks for the virtual desktop hint, I'll have to try it, maybe I can work something out with that...
Thanks for your answers.