At the moment there's very little orphaning of blocks, and next to no occurrence of two-block side chains. Unless you're dealing with large amounts (larger than two block rewards worth, probably), your chances of attack are incredibly incredibly low. If you're dealing with amounts less than a few BTC, I'd personally be happy accepting one-confirmation transactions.
There's no specific flags for
bitcoind that you can use to control confirmations, it's all in your software's side. Generally if you're a merchant, you should avoid having a listening node (set
listen=0) just to be on the safe side. Be sure to be using cold storage if your server accumulates a target-worthy amount of currency, by sending off to an address that the server does not know the private key of.
If you're not using
walletnotify to control your internal accounting system, you probably should.