I have never been much of a dieter, but I can answer your first question.
Do your cardio first thing in the morning, on an empty stomach or light, light meal. Since your goal is weight loss along with muscle toning, you will be able to target energy stores as your source instead of what's in your GI/blood at the time.
I think the logic behind the carbs/morning//protein/evening is that you will burn the carbs throughout the day while you have an elevated metabolism and are working out. At night your metabolism lowers so it would be more ideal to have protein, that won't be stored as fat and instead go toward muscle development or just waste, in your system.