[BassKozz]

Ok I finally switched from "Separate X-Sessions" to "TwinView" and I am loving it, but this problem with applications opening up in the wrong monitor still exists (as darthmob mentioned).

I think everything defaults to the Primary monitor, and I have to physically move applications over to the secondary monitor even if I've clicked on the desktop icon in the secondary monitor. Also now that I am not using "Separate X-Sessions" the panel bars only exist in the primary monitor so I can't run applications from the panel bar in my secondary monitor....Is there a way to have the panels expand across both monitors?

Is there a solution available out there?

Another pain-in-the-ar$e is that I like to watch videos (using VLC) on my secondary monitor, but when I select "Full Screen" from within VLC it automatically defaults the full screen to my primary monitor, even if the VLC window resides in my secondary monitor... Is there a way around this?
UPDATE:p.s. This also happens when I am watching a video in FireFox (i.e. YouTube) and I click to make it full-screen, it opens up the full screen in the other (primary) monitor even if the FireFox window is in the secondary monitor.