Business & farm

So boxes 4 and 6 are empty on my W-2. However, according to our payroll person, he said the amount in box 2 was taken out for social security throughout the year for my housing allowance. Does that even make sense? If so, does that mean I've already paid that? It seems like all the other forums on this type of question show that number 4 is the correct response. I just want to make sure as the amount changes dramatically when I select different options. The only other response I think might be appropriate is to pay self-employment tax on wages only.