SSF is your subsonic filter. This means that you want to set it for the lowest frequency roll-off, not the highest. I believe most of them go down to about 15Hz or so, some are 7Hz. Now regarding the gain, this is not for "volume" as you mentioned, "will is be only getting half the power". Not really. The voltage is related to power output, but is not parallel to it. The voltage should be matched with the output voltage of the preamp, or receiver, or cd player(car). Some of them go up to about 9V, but most I believe are around 2V low level output. This is related to the distortion you may be getting as well, even though this was not mentioned, Im sure with the settings you have it at, it is there....even if you cannot heard it. When this distortion is minimal, and the voltage is matched, the response will be better, and the "sound" overall will be cleaner.
It's like this.........you ever hear a factory system from the outside of the vehicle and all you hear is distortion? And when they turn it down a little and the distortion goes away, but the output remains the same audible level? It's like that. If it is not matched, your feeding it more distortion than clean power, which will in turn affect the overall response curve, hence cancelled frequencies. Some of it has to do with resonances, but in your case, the more important factor is the distortion levels and matching the input output levels. The gain should be used for this, not power, or to gain more power, as it really only increases sensitivity, or applied voltage-to a point.
So, if you have that "factory" type of sound or setup, you will notice that when you run out of applied power, the distortion will kick in, such as in using a bass boost, where it may appear to create more bass...it is actually increasing sensitivity, which can cause the distortion. When you set everything right, you should not hear a loss in output, but cleaner output, as that loss is what you were worried about with the 2V amplifier sensitivity setting vs all the way up type of situation.
Hope this helps.