A 0dB tone give maximum output from your head unit because it is the highest level source signal. The benefit of using 0dB tones is that no mater what the recording level of the music, it can never exceed that signal level and if your amp is not clipping with a 0dB tone it cannot possibly clip on music.
The drawback of using 0dB tones is that the vastly overwhelming majority of music does not approach 0dB in recording level even on the loudest transients. What that means is that you have amplifier potential that you are not using because the signal from the music is never getting to the level that you used to set the amp. Using a 3dB tone lets you get some of that back and since most music doesn't get to -3dB either you still usually have a margin of safety.
To determine whether or not 40hz is the right freq we have to know where your crossover is set. As long as the crossover is set a good bit higher while you're setting the gain and you don't have a subsonic filter engaged, 40hz is just fine.
As far as the dimming, the power rating of your sub has no bearing on that, only the actual power output of your amp and its efficiency. As already suggested, the Big 3 is your first step. If you're still having problems after that, make sure that your battery is good. If it is, you might start considering adding a second battery. With a 1kW Class D amp that shouldn't be needed.