After you file

You do have a choice.  You can pay the fees upfront with a credit card or have the fees deducted from your refund for an extra $40 Refund Processing Service charge (45 in California).  

If you pay with a credit card your refund comes directly from the IRS.  If you have the fees deducted then it goes through the 3rd party bank which costs more and may add a day or two.