I have a JL Audio 500/1 amp for my W7.

I plan on setting the gain on the amp with the volt meter and tutorial that jl audio has.

my question is, once i set the gain to the maximum level it needs to be at, will it be bad for the subwoofer if i was to increase the "Subwoofer Level" from the head unit?

 

as long as the gain is set on the amp to a nominal level the hu level will not affect it...

 

You can send the sub-woofer's amp into clipping and over drive your woofer burning it out. Understand that the amplifier is designed to take a certain maximum input voltage. Beyond that point the input stages become first non-linear and then start to clip - cutting the tops and bottoms off all those nice sine waves creating distortion. Massive distortion. The kind that makes me want to rip my eyeballs out distortion. Most people can't here 8-10% THD ... my skin crawls at 2-3%.

Other that sounding bad the other "benefit" of clipping is the creation of odd order harmonics. Those are overtones that make the musical instrument sound out-of-tune. Like the difference between Eric Clapton playing a $10,000 Martin and your 12 year old brother play an $80 plastic guitar.

And finally the best "benefit" of clipping is that the subwoofer motor is designed to dissipate X number of watts of sine waves - those nice smooth things cause the speaker to move back and forth. The same wattage of clipped square waves has a higher amount of RMS voltage (RMS is a measurement of a sine wave and is equal to 0.707 of the peak voltage) and as the woofer operates it pops back and forth between places where it pauses to stop making music (sine waves) and makes HEAT instead - heat is what melts coils and causes the glue holding the motor to the spider and basket to come apart.