Ok, I finally got all the wires hooked up. Yes I have the same 3 pins but the 3rd one in is already occupied in the harness that goes to the door, so only the last 2 are for the speaker. The rear left behind the driver side speaker, positive wire should be "Green" & Negative should be "Green/Black". The rear right behind the passenger side speaker, positive should be "White" & Negative should be "Blue/Black".
The way I hooked them up is I used some pin connectors I had laying around from a Honda harness and put the in the corresponding pin slots so it looks like its still from the factory. Only thing is I'm going to have to use my alpine type-r brackets since there isn't any on the LS model and I would need to drill holes so I can mount them because there isn't any holes made from factory.