I've been told differently, and actually saw differently...I bought my first 5S from Best Buy, and saw the woman beside me trade in a 4S and a Note 2 for the 5S. They never said a word about it and she was done and out the door before I was. I also asked while waiting for my info to process if I could trade both my iPhone's (i had my personal and work phones with me when I bought my first 5S) in and the clerk said "Yup! Just have to do some paper work!" Now I had no intention of doing that, I was just curious, but it seemed they were eager and willing.
My case could have been unique...but I would contact your local Best Buy to see for certain.
Also, just to put this out there...while Best Buy is offering the best trade in that I've seen around the web...trading in your iPhone is silly compared to selling it on the private market.