I'm assuming that the dual exhaust is after the catalytic converters. This doesn't necessarily require a tune, but it's definitely going to be worth it. There's no doubt that a Bama custom tuned SCT X3 is going to be the best modification that you can do for your Mustang. Also, it's something that you'll use as you add modifications down the road.
If you have absolutely any questions, whatsoever, please feel free to give Bama a call directly. They're here in the building Monday-Friday from 9AM-5:30PM EST to answer technical questions and explain the whole process. Give them a shout directly and they'll hook you up! 888.226.9764
Good luck!