I have no idea how these certificates are "supposed" to work, but my results have been great.
Had two days worth months ago, applied them to a rental at SFO. I would have expected my 4-day rental to only give me 2 days credit (since I got 2 free), but I got 4.
Just rented in Chicago, expected to get the value of the great rate I got credited, but they credited me with the much higher same day/walk up rate, so more money off than I expected.
I DO always put BCFD in the discount box (because they say to), so I don't know if not doing it would work, but I've been very happy with the results playing by their rules.