From the P!P Website:
So it is MD-On for nationals, discuss!
http://www.pokemon.com/us/organized-play/championship-series/2011-national-championships/faq/WHAT IS THE TOURNAMENT STRUCTURE?
The tournament is run using the Modified (MD-on) Format and Swiss plus Single Elimination.
The National Championships will be broken into groups by age divisions and will be run using Swiss Pairings. Because Swiss rounds are dependent upon total attendance of each age division, Swiss rounds will be announced on site. Swiss rounds will feature one-game matches.
After the final round of Swiss, the top players from each age division (depending on attendance levels) will move into a single-elimination round. Single-elimination rounds will be a best-of-three game format and will have a 60-minute time limit per match.
National Championships events have a K-Value of 32. For more information on K-Value and Ratings and Rankings, click here.
So it is MD-On for nationals, discuss!