So, unplugged the amp and nothing changed. All speakers still functioned the same except for the 6x9's. Phoned an audio shop that I was referred to and an installer there also told me that the little amp is only for the 6x9's. I inspected my amp and found that the board was severely corroded due to a leak that is apparently common from the firewall and shorts out these little bastards. So, now I just have to decode the wires and find out which ones run back to the 6x9's and wire them back up!