You can set Commission on a trade-by-trade basis, and not on an order-by-order basis. My (overly complex) workaround from my blog attempts to address this.

In other news, you can always use Interactive Brokers' SMART Prefer Rebate or SMART Maximize Rebate routing options. With these, you can place limit orders that add liquidity, and you might actually get paid for order fills (if there are exchanges that do this for the given instrument, I think some stock exchanges do).