as far as the wireing goes ur basically saying i need this converter to convert the f/r l/r to a single output. can i just tap into my rear speakers for the power for the signal?
If you tap into the line going from the H/U to the amp you will not need the converter because I believe they are already a low level input. Meaning it has the same signal as an RCA. It would be an unfiltered signal as well (except for what you can control in the H/U; bass, treble, etc.). If you are going to tap into anything in the trunk I would tap into the wire running into the sub rather than the rear speakers.
Personally, I always suggest, for the cobalts, to replace your factory h/u if you want to run subs. It will be that much better and if you follow my h/u how to you can install it and keep your factory amp for under $50, if you make your own harness.
theres no rca's running to the factory amp/sub?
No, GM uses the standard harness to send a low level signal (RCA) to the amp. Essentially with the non Pioneer sound system those wires run to the speakers, but with the Pioneer they are split at the amp and the low level travels to the amp and the high level signal (speaker signal) travels from the amp the rest of the way.
as for wireing, its okay to just tap the power and ground directly to the battery in the trunk right?
Yeah. That is what is nice about having the battery in the trunk.
and also what about a remote signal for the amp to turn it on when the stock HU comes on?
This is actually difficult with the stock amp. GM uses their new wiring system (named GMLAN) in the cobalt and it doesn't use the traditional remote turn on. You will have to grab an accesory power to turn the amp on and off with the car. I don't know of anyway to turn it on and off with the stock H/U. I go over that in my how to as well.