I did a 16-man heads up tourney last fall, in two stages.
First stage was pool play. Randomly drew four pools (clubs, diamonds, hearts, spades) of 4 players each. Within each pool, each player played the other three in his pool. This way I guaranteed each player at least 3 matches for his entry fee, and avoided a "fluke" outcome with stronger or weaker players.
Second stage was an 8 person single elimination tourney. I "seeded" a bit in that the winners of each pool, by record with tiebreakers, played the 2nd place man from another pool. I also structured the bracket so that the reps of a pool (e.g., the diamonds pool) could not meet again until the heads up championship.
The whole thing took about 8 hours, but part of that was because I froze the blinds too soon within some pool matches and at least two went past the 2 hour mark. When we run it again, the blinds will go up another few levels and those games would end sooner.
Hope that helps. Let me know if you have other questions.
Ryan