There is probably a decent way to communicate to users that the corners are hot, probably via some animation.
For example, running apps are available from the left hand side. When an app disappears (eg. hitting the Windows key), just having it slide over (perhaps even popping out the running windows to see it slot in) would communicate where you need to look for things.
The RHS charms are probably harder, but I think there's a way to do this given a little extra polish.
That's actually exactly how it was designed in the Developer Preview, and for just that reason. Every time you pulled up the Start screen from with an app, the app would slide to the left as a hint it was available there.
The problem was that the sliding animation just gave you a headache after a while, especially using the start screen from the desktop. So in the Consumer Preview it was replaced with a more subtle fade-ish animation, making it less apparent where the app went but protecting the user's long-term sanity.
For example, running apps are available from the left hand side. When an app disappears (eg. hitting the Windows key), just having it slide over (perhaps even popping out the running windows to see it slot in) would communicate where you need to look for things.
The RHS charms are probably harder, but I think there's a way to do this given a little extra polish.