My first idea was to have the button on the top left stay green if an incarnate slot was active, much the same as the popup button will stay green if popups are active. Then I thought that having the same sort of button to toggle them all on and off might be a better way to go, though I have no idea how hard it might be to do.
The way things are right now, there is nothing to indicate whether a slot is active or not. We can toggle armors and defensive powers on and off, but Incarnate slots are an all or nothing sort of thing. Any chance of that changing in the future?