I've found that using Loudness is the best way to add kick to those songs that need it. It uses a special algorithm to increase the lower frequencies without distorting the upper ones. It is better than just Bass control or the fader because it "does the right thing" if you are trying to get more kick out of your subs. Adjusting the EQ and Bass is intended to be a 'set and forget' thing... The EQ tries to make your car sound good at all frequencies and the Bass for adjusting the song to match what you think it should sound like (i.e. it was mastered wrong for your car).
I used to use the fader to do exactly what you were doing untill I got used to playing with the Loudness (and found the gain sweet-spot on Sub-amp). Besides, Loudness just a single long-knob-press away with Hijack.
Adjusting the gain on a sub-amp is strange because you think you want it 'as high as possible' so you can get as much bang for your buck... but in reality, you want to adjust it so it matches the rest of your system. So when you adjust the volume, the sub adjusts at the same rate (i.e. acceptable bump at high volumes, and loud enough so it is still around at low volumes). By having the fader all the way forward, you are attenuating the signal as much as possible (i.e. as close to negative (-)infinity). Everything to do with sound is logarithmic; the fader attenuation is doing it's best to make useful adustable steps, but the steps will always be more extreme (and inaccurate) at the maximum setting.
You could also use the EQ (in 4 channel mode) to adjust the subwoofer 'gain'. (
FAQ ) You are probably already doing something like that anyway. If not, you should seriously consider remapping the Q values (basically, the steps that the EQ sees) so you can tune the low frequencies to the characteristics of your Sub+enclosure. Otherwise, you can adjust the fronts (= all normal speakers) down (-) by a few db so the dynamic range for the sub is 'more' than the rest of the system.
The philosophy behind sound calibration is to attenuate as little as possible because it is never perfect (or linear - the same across all frequencies and amplifications). Never amplify (+ EQ) if you can avoid it, always Attenuate (- EQ)
But, if you can, Tony's suggestions about adjusting the gain on the sub-amp is "the right way" to do it.