When we ran ours we ran it in pods of 4. Luckily we had 12 show, so numbers worked out well. If you get more just make the larger pods the losers brackets.We did rounds that were 1hr long (I think it was 1hr, no 5 turns). If you won your table you got 3 points, if you were alive and time ran out it was 2 points, and if you played the whole round until dead you got a point. The most points won after 3 rounds.
The reasoning behind the 1 point for playing out a round was to stop random things like someone swinging w/ sword of feast and famine and the person they are attacking scoops because they are going to die but then the attacker doesn't get to untap lands, etc. Also if i have 20 power of attackers and you have no blockers you might scoop because if I attack you then you would die, but this allows me to attack someone else an essentially get a relentless assault for free.
One big issue one person had was their strategy. They went full out and blew two people out in a game, but I managed to shut down their attack plan and beat them. They felt they should have gotten something more then myself because they defeated two players at the table while I only took him out. I think it was just poor decisions on his part to kill people that could have helped kill me, but his view point might be worth taking into consideration.
It is an EDH tournament, do what your players want you to do, that's what this format is all about. Tournament do tend to take a little of the fun out of it though.
[Edited 1 times, lastly by caquaa on July 31, 2011]