The Juice Box is designed specifically for use with the Two Brothers exhaust, at least that's the way it was when I was doing the same thing you are doing right now. Power Commander is easily interfaced to be used with any exhaust. The PC has more support and tuners that work with and have extensive knowledge with the product.
Having said that, all of that could have changed by now as I have had my PCV for three years. It is super easy to use and I have not had any problems with mine at all. Hope this helps.