Problem with, ?headunit?

Alright, so I'm going to post a diagram and explain exactly what happened, hopefully someone can help me. I'm going to start by saying that everything was working, my head unit made noise in all of my speakers and subs except for the rear left speaker. The head unit harness has a faulty connection to that one speaker and i don't know how to fix it. But, I have an amp with four channels. Channels 1&2 receive input from "SUB OUT" on the back of my head unit. Then on the amp channels 1&2 put the bass to my subs. Okay. That's all normal and good. So now for the F'd up part. I decided that since I can't fix the harness on the head unit, I could use the amp to run my rear speakers. I had heard of people doing this for better sound quality, but never for fixing a faulty wire harness connection. Channels 3 & 4 aren't being used anyway, so that should all work fine. I got another set of wires, and from "RCA OUT" on my head unit, i connected them to input Channels 3&4. I used; just to see if this setup was all going to work (temporary) telephone wire to go from the amp to my rear speakers. From output 3&4 which was now receiving from RCA OUT on my head unit. I checked, everything was hooked up right, and connected properly for a test run to make sure it worked. I turned my key backwards, and my subs made an awful noise as if they were dying, it's hard to explain in typing, but it wasn't a bass hit or anything it was just sub-death. But, that's not even the bad part, absolutely none of my speakers were working at all aside from my sub. I turned the key off, unplugged the RCA OUT and the input for Channels 3&4 cable, unhooked the telephone wire that ran from the amp to the rear speakers and tried again, back to having all wires in the functioning position where all my speakers work. But, nothing works at all except my sub now. I can't figure out what happened to cause all of my speakers to stop working. I know this is long, but I feel the need to be very descriptive so whoever may be able to help me has a good understanding of exactly what I did.