For the basics I'd start with the following:
Start with a $100 or $200 salary cap
Bid in increments of $1
Decide on open or poker style - open you can bid at any time, poker is once you pass you are not allowed to bid on that player again.
Sit around a table or have some sort of order for nominations. We just sit down at the table and have last years champion start and go clockwise from there for nominations.
As Commish create a spreadsheet to track cap spend and cap left to spend - this is important so that you don't have owners spend all their money on 10 players. Usually it is required to keep at least $1 in your salary cap for each open roster spot.
Discuss the auction process before you start. Make sure owners are clear on the process and the rules of the auction.
If poker style decide how much time an owner has to bid or pass
If open decide how the final sale is determined, once, twice, sold or going, going, gone - some advise using an auctioneer not in the league to do this.
Find a nice place to have it and enjoy. Auctions are a lot of fun.
This is all that comes mind on the basics. Do a search for fantasy football auctions, fantasy football auction strategy, etc and you'll find a bunch of auction articles. Of course there are also some pretty good threads here on the cafe as well.
Hope this helps. If I think of anything else I'll add to the post.
Fatalism Helps with the Jump but not the Fall