Sounds like you've got it. The wires that go to the rectangular plug that plugs into the amp go to the speakers, with the exception of some of them, which are amp power and turn on.

1999 Mystique LS V6 Alpine CDA-9807, Rear deck sub, Opt. TB, K&N RU-3530/MAF adaptor, custom heatshield, FSVT 17's, SCT 4-program chip, Eibach's/ST200's, Hella Fogs...