The way it works is you can choose one item you want to auction for and offer as much as you like in the hopes of getting it. They process these, and based on maximum bid prices, and lower bid prices as well, many items go out via this method. I forget the actual calculation on how they determine cost, but it has to do with your lower bid price plus some variable of your maximum over someone else's maximum. I never really understood the point of the lower bid price, as the maximum bid is the one that determines who gets the cel.
Of the items left which nobody tried to get by offering the most, they lottery them. Sadly, I have heard from many people 'in the know' like the infamous P website and others, the lottery isn't actually random by any means. Still, it can be worth a shot.
I remember doing a Mandarake auction at their Nakano store. It was one of the cels in the case, and you just dropped your high bid in a box in the store and the highest bid got it. I spend forever trying to come up with a good price, and the night the auction ended I was there and the price listed in the window as 'high bid' was still lower than mine. I went in the next day and the sign said 'sold for xxxx' which was still lower than my max bid, however when I went to pay for it, they told me someone else had won it. I asked how that was possible when my bid was higher than the amount in the window and they said the amount was a mistake or something along those lines.
I never really understood it, I was only bummed at missing the cel. Now I don't try to understand how their process works, but luckily haven't seen anything in about a year I had a real itching to go for.