We do a re-draft auction every year and have had great success with doing the following:
1) The #1 rule - make sure you (the commissioner) are NOT involved in the physical functions of the auction as you will need to tend to your own team. You will need an auctioneer and a helper. The commissioner will still be in charge (breaks, disputes, etc.) but can not be loaded down with being the auctioneer if he wants to have a decent team and have his sanity by the end of the day.
2) Make sure your auctioneer is consistent. And what I mean by that is this:
-For the 1st 50 picks or so he should be fairly deliberate in order to allow everyone time to spend their money.
-Picks 50-150 or so he should pick up the pace but still give some time after the name is called for everyone to look up the player or you'll be there all day.
-Towards the end of the auction he needs to really pick up the pace as money is scarce and many have already filled positions that are called out.
3) If you are putting stickers up on a board with the player names, writing them down, or entering them into a computer you will need a second man for this job (the helper), making sure this person knows all the players and positions. This allows the auctioneer to keep the auction rolling.
4) Have the league put up $5-$10 extra each (believe me - it's worth every penny) to pay to the auctioneer and helper for their work for the day and buy their lunch and sodas (avoid beer as they needs to remain strong, especially late in the day).
5) Breaks - it's very important to allow breaks. We have between 3-4 10 minute breaks, allowing everyone to use the restroom and regroup their thoughts heading into the next session.
This should get you going; if I think of anything more of great importance I'll post for ya