I'd have a hard time getting out six days a week. There's nothing wrong with going for a two mile run after your workout.
I would normally do no less than 45 minutes in the gym. I like to leave feeling tired/depleted. And to do that in 30 minutes is difficult for me.
I don't know the benefits of protein over regular food. I take Optimum Nutrition after workouts mixed with yogurt (Activia), milk, chia seed, flax seed and frozen fruit. Or, if I'm hungry I just eat a meal. It's hard to get full on the shakes afterward, so you can end up eating more to satiate your hunger.
In general, I don't worry about cardio affecting my muscle building. That may be why I'm not bigger, but I still see gains.
I think it's a great idea to start with a circuit. Then, when you get tired of that or just don't feel like you're making gains, switching to a split routine is a good idea, like you have planned. I usually throw in one or two leg workouts every day I go to the gym in lieu of doing a "leg day". 1) It's way easier to skip going to the gym on leg day cuz I hate it. 2) It keeps your from dessimating your muscles, which is easy to do with legs, and affecting other activities (sports).
Also, as you start to add muscle and do weight training you'll lose fat. I think weight training is just as good as some cardio for burning fat.