When i installed an aftermarket player and followed the colormatching, all the speakers I thought were working. I pulled the harness out of the amp under the cc unit that matched the harness I bought from an audio store. However, I noticed that my factory subs arent working after the installation. I have the 8 speaker system and six of 8 are working. I read the pdf file about sound installation but it doesnt get to the part about another amp under the chair. Is there something else I need to do? With the amp under the chair, do I need another special harness? Can somebody give me some good details about how to wire it neatly? I was going to splice the sub wires and just run a wire but I wanna keep it clean and as close to stock as possible.

You can get an amp integration wiring harness from metra to run all the speakers. When I put my new head unit in I just bought the regular toyota harness and got an external amp to run the subs.

This has been discussed in detail several times before. Try searching.