They do a parallel contest for employees only at the same time - not AHA/BJCP sanctioned. They take the top three from that competition and have an audience at the GABF taste and vote for the final winner.
The Brewing Network
had an interview with Jim Koch in January, who talked about the contest at length. He's a great guy who just loves beer, and is really excited about the contest. Worth a listen, especially if you're thinking about entering this year.