You only need a deposit for the auctions. This is in case the auction is won but the client can't pay, so they can recoup their losses.
You got the right to bid up to 3 times your deposit for an auction. So, in your example, I'd say you'd have to put around a 6000 yen deposit to be sure. Also, note : the deposit is completely separate from the payment of the auction, but you can ask for you deposit back any time you want.
I use noppin both for auction and for shopping, never had any problem with them.