Is this for a flight from Miami to Germany? Where in Germany? What time of year? I always check ITA Matrix Search for the best fares. If you haven't, you might try it. I experimented with RT Miami to Frankfurt in January, and Air Berlin with one stop was 50% higher than some others who had non-stop flights. Here's the link to check things out: http://matrix.itasoftware.com/.
You can play with the search boxes until you get an option you like. It will spit out an itinerary with all the pertinent details and code numbers to make reservations with whatever airline you choose. Print it out to refer to. Then you get to make the reservation with them. If you don't see the same options when you search their database, call them. And if Air Berlin is your choice, you can find out about the seat charge when you talk to them.
We flew Air Berlin from Florence to Stuttgart in June, 2011. We got assigned seats at no extra charge, but that was 2.5 years ago and within Europe. I made the reservations online from here before we went. For what it's worth, maybe nothing, I never book through a 3rd party. It's just gets too complicated if something goes wrong.