Anyone have any dual monitor workspace presets they like? I tried creating one, but it's kind of clunky. When I spread the workspace to the left monitor and break up the frames, the left side doesn't go all the way to the top. It stops at the same line as the right monitor's Mac Menu bar. I also noticed, that programs behind the frames (Firefox, etc) don't come forward if I click on them. I can see them behind the After Effect's frames. That's doesn't seem to be right.
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).