Setting JL Audio 1000/1V2 with SMD DD1

[Swingnamiss22]

I just purchased the SMD DD1 and SMD CC1 together. I have the JL Audio 1000/1V2 running my JL 13.5W7 and the JL HD600/4 running my JL C5 650 components. I have this hook up in my 2003 Yukon w/ Bose system. The problem I'm having is where do I connect the negative alligator clip? Also my HU is the Pioneer Avic z130bt. After going through the process my amp gain is barely up when setting it with the SMD DD1. After disconnecting my speaker leads to set the gains I realize that the factory Bose sub is still connected as well as the tweeters and i think they r running off the HU. Would this cause problems?