Stock amp in the boot

[lekodey]

Got an AU SII Ghia that had Premium Sound in it up until a month ago, that crapped out so I went and bought a Sony CDX-GT370 on the basis that it was cheap, looked good and it said it did whatever I needed it to. Not big on this sort of thing after all. Now for my question...this has since been installed...decently enough...albeit with no working aerial...because two wires don't go into one in my logical mind and minus the amp/sub. The aerial i'm fine with not having since radio isn't an issue, however the distinct lack of any bass is slightly annoying, from what I see of my wiring...the amp has red/yellow/black coming out along with what appears to be an rca? and two grey cables. No there is also a plug in the front that appears to have...red/yellow/black along with another random plug. The main loom has 3 spare wires left over that I couldn't identify, so now after that dodgy explanation i'm wondering whether anyone has used the stock amp in the back...successfully with an aftermarket head unit. If so...how, my head unit has the amp rem lead on it...but just the one...so i've got a feeling running the amp has something to do with either the rca looking plug or the red/yellow/black. My problem is only made more complex by a lack of knowledge, since i've never had to deal with an amp before. I know how the amp rem lead is supposed to control the amp which in turn controls the sub. All the speakers are stock so I see no issue with running them through the head unit...I hardly think they will need more than the 52 per channel or so that it gives. So I just need to know what the hell I hook up to the damn amp remote. Can go out and look at things and take notes if more info is needed, which i'm guessing will be.
I would really appreciate any help anyone can offer. Thanks guys.