Here are the basics:
E-Bay Style
36 hour timer
No limit on the number of players up for auction at any given time.
Warning this will get crazy, just be prepared for crazyness!! You can bid on up to 25 players at a time but you can't ever bid more than your salary cap at any given time.

Proxy Bidding, think ebay again here, the timer is reset each time there is a new high bid.

Here's a detailed example of how proxy bidding works. Let's assume your league is set up (on the "for commissioners > setup > auction setup" page) with the following parameters:

Minimum Opening Bid: $1.00

Minimum Bid Raise: $0.25

Let's assume that Franchise 1 opens bidding on Player A, and the initial bid is $5.00. The system will "remember" the maximum bid of $5.00, and report the initial bid on this player equal to the "Minimum Opening Bid" of $1.00.

Then, Franchise 2 submits a bid of $2.00 on Player A. The system recognizes that Franchise 1 was willing to pay up to $5.00 for Player A, so immediately after Franchise 2 submits his $2.00 bid, the system notifies him that he has been outbid, and then considers the high bid on Player A to be $2.00. Then, Franchise 2 submits a bid of $5.00 on Player A. The system recognizes that this bid amount is equal to the maximum bid made by Franchise 1, so the system then considers Franchise 2 to be immediately out-bid (earlier bids always beat later bids of the same amount), but the system then considers the current bid amount for Player A to be $5.00 (the maximum amount that Franchise 1 was willing to bid).

In other words, this "proxy" bidding configuration allows a franchise owner to bid only as much as he needs to on any given player, and no more.