We just upgraded my wife's 6s Plus to a 7 Plus last night at our local Apple Store. It was very easy, just walked in and told them she was eligible for an upgrade and after they verified that her phone was eligible, she got her new phone.
It might be a little different if you're trying to do the upgrade around launch time. I'm in the same boat myself, looking at either September or October for my upgrade from my 7 plus.