There's not really a Metro Mode and a desktop mode, there's only one mode. You get one main app taking up most/all of the screen + optionally one companion app on the side. The desktop acts like an app and can be in either of these positions (hence why it's not really a separate mode) and within the desktop, you can run as many (desktop) apps and windows as you like and have the taskbar etc etc just as before, with the exception that the start menu has been replaced with the start screen, where you can pin, launch and switch to both the new kind of apps, the desktop as a whole, and individual desktop apps (which switch to the desktop and launch/switch to the app).

You're correct that desktop apps and the new kind of apps are separate (with the exception of web browsers which have a bizarre way they can run in both environments).