i have my main icons and everything on the left of the left screen (primary) where you'd expect them and run any games i can in windowed, i keep my taskbar on the right so i can still toggle between apps and things without windows menu effects coming over my game window stuttering the pc to 0.5fps. i generally have my right monitor full of msn windows and do everything else on the left, ie the more important it is the further left of my screen goes.
having the taskbao on the right also means windows apps can fill the whole screen, nit just down to the taskbar, and i can still see the taskbar.
there is no way i am aware of to prevetn a fullscreene app minimizing when it loses focus, just use maximised windowed games where posible, if you have to run at a lower resolution that you normally have the screen it isn't much hassle to drop the resolution to make the window fill the screen.