Methods for treating atrial arrhythmias can involve configuring an implantable arrhythmia treatment device. A device can be configured after implantation when the patient is fully conscious and after any pain suppression medication has worn off. The device is caused to apply a phased unpinning far field therapy to the patient in response to detection of an arrhythmia via a far field configuration of electrodes. An indication of a pain sensation of the patient and the effectiveness of the treatment in response to the therapy can then be received. In response, at least one of a set of therapy parameters is adjusted and the steps are repeated until it is determined that an effective treatment is provide at a pain sensation that is tolerable to the patient. The device is then programmed to automatically treat arrhythmias detected in the patient with the determined set of therapy parameters.