Are your two monitors the same size and resolution? It sounds like you haven't cofigured them in Display Preferences to align at the top.
Re: windows not coming forward, get used to using Alt-Tab or the Dock icons to switch between applications, rather than just clicking on background windows. It's a failing of OS X that all active windows don't come forward when you click on a window in a different app. Alternately, and my preference, use different workspaces and just flip between them with three-finger swipes.
Same size/resolution. Don't have problems with other programs that are dual screen (FCP, Avid).