Stock HK wiring questions

Last weekend I installed an Xtant 121M sub amp and a 12" Boston Acoustics sub. I tapped into the stock HK sub wiring harness and used the green and blue/green wires for the sub input. The thing I noticed is that the voltage of these wires is VERY low. I had to set the amp to the 100mv - 300mv input voltage setting and even then the gain must be all the way up. I am not very happy with this arrangement since I know this gives me more distortion. Anyways, my questions is if I tap into the main amps wiring harness would I find that the voltage is higher in the leads for that amp?

Also in the sub wiring harness, what does the thin black/green wire do?