replacing the speakers will give you better result than a new HU. but if you want the aux then i guess you got a reason to replace your HU

 

bass with a sub doesnt have to rattle your car.

 

can i hook the two amp channels that im not using to my factory rear speakers?

 

You can but it would be pointless because from the way it sounds your cd player is allready giving them a little to much power. If you have a 4 channel amp then which amp do you have? Model number would help the most. I suggest you take the subs out of your car and buy a decent set of componets for the front doors then just a good quality set of 2-way speakers for the rear. Use your amp to power these and not the subs.

I am firm in thinking for people that just want a decent sound audio system that aftermarket speakers are bar none the best invest ment you can make, they are more efficient, have wide freq bands, and handle abuse alot better than the stock speakers. More times than not stock speakers are paper based cones and made for background noise alone.

 

If you have the two spare channels on the 4 ch amp, then the most cost efficient option I would recommend would be to get a new pair of speakers for the front, and push those off of the 2 channels of the amp.

Of course the best option that I would recommend is to replace all four speakers and run those off of the 4 channel, and also get another small mono amp to push the subwoofer, so that you maintain a equal eq response curve.