No question that a 2 into 1 pipe is a great choice for Dyna's and you shouldn't have any "rubbing' issues as long as you get the correct pipe for your bike and it's not lowered. A lowered bike can create issues with any pipe, so you will have to look into that on your own.
I suggest a D&D Fat Cat for a 2 into 1 pipe, I think it's the best one on the market personally.