I would really need to see your headunit's rear panel to make sure you can do what I did, but if you have two sets of RCA preouts on the back, you can do it my way.
For the subwoofer, the head unit somewhere (either in its function menu or an actual switch somewhere) should have a setting that allows you to switch the rear output between full-range sound and subwoofer sound. Setting it to subwoofer sound is best, but if you can't/don't that's okay. You hook up the RCA's for the subwoofer amp to the rear RCA preouts on the head unit and make sure you use the LPF (low pass filter) on the subwoofer's amp to filter all the high frequencies out of the sub's signal. This way you won't damage your sub or overwork your amp trying to play music your subwoofer can't handle.
For the regular speakers, you would need to use the front RCA preouts and get two splitters to turn your two RCA preouts into four, like these:
http://www.crutchfield.com/p_119ILJR...r.html?tp=1934
Once you have four preouts you can then plug up the corresponding RCA plugs from the cannon plug adapter that came with the amp integration harness. That should give you sound to all seven speakers. Of course the blue remote wire on the cannon plug harness needs to be wired into the blue wire on the square harness, which gets wired to the blue wire on your head unit's harness. That should give the amp power and you should be good to go (I think you've done this though if you have any speakers working). On to the next problem...
Check the speakers for proper connections there at the speakers, I had that happen on my old G when Circuit City did a poor solder job on my door speakers and I had to fix them myself. Check connections at the amp under the seat. Check the wires at the speaker ends with a DMM with music playing to see what your voltages look like to make sure you have power going to them and it's not the speakers themselves being bad. And of course make sure you have the head unit set right and the rears actually having signal. Again, with pictures of what you're working with I'll know for sure how to proceed, but this should get you started. If you have any more questions, feel free to ask, I'll help as much as I can. Good luck!
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