Those speaker wires are to pick up input from a stock head unit or really cheesy aftermarket one with no sub out. For that sort of install they just connect in parallel with the rear speakers.

If it has an RCA input run that to the sub out of your head unit and remove the speaker wires from the other input.

 

Take pics! All subs have speaker wire, since it is a speaker... Run them to an amplifier, and if it has an internal amplifier then it will take RCA. It could possibly not be an amplifier in there, it could be a cross over in which case its function it to take out the high end of the frequency put out by the amplifier so that the sub always plays only sub level sounds. An amplifier could potentially take speaker wire input and just amplify the signal, in that case I would suggest replacing it with a batter amplifier.

 

i know im late on this..so bear with me.im a stereo head case...
.....look up "the big three" on youtube.this is a tutorial on you running a thicker gauge wire in 3 places as follows.from chassy to block,(i did this twice,2 sepperate wires in different spots)1 from the ground on the battery to the chassy,and 1 from the alt. to the main possative terminal on the battery.i reccomend doing this with 0 gauge wire,but 4 gauge will do as long as your not gonna run too much wattage...4 gauge is good for up to around 1500 watts or so.make sure your chassy grounds are paint free,scuff down to the bare metal.i bought nice gold connectors for the battery,with the extra 0 and 4 gauge intput for 15 bucks off ebay.just doing this alone will help with better current supply to that kenwood,which is more then likely why your car was dying.do to TOO much draw from the entire charging system will kill your engine.
now if your gonna run more(i do)spend 20bucks on a relay to run dual batteries(relay makes sure your alt charges both properly).i run 2 deep cycles in my trunk for the sound system alone.this creates a spot for the amps to be ran from the trunk(i.e. less wire running thru firewall)not the engine compartment.now i will go into why i did it this way.
in my opinion caps are a waste of money,or at best,a bandaid fix.they dispurse all there energy in 1 base hit,then need to charge back up to continue the process.this creates a constant draw on a system that was already lacking in the first place.1 battery with 800 coldcrank is the equivolent of a 100 farad cap!you would need 1 farad per 1000 watts,you do the math.its so much cheaper to do it th right way,and your lights wont dim,the extra battery is there if your exzisting battery craps out,it will sart your car.
if thats not enough ampreage,then your really pumping out some watts,i recommend you get a 150 to 200 amp alt to charge all the above(if you do this you'll need a relay that is rated for 200 amps).all this can be done on the cheap,i had most of the wiring and the deep cycles already.
i run this system with a stock alt and 80 amp relay,3 batteries.i run 1 kenwood 1800 watter,and a 200 watt deck,rms is less then 1000.im still putting together all the pieces,so ill post pics on a thread soon to show how and what..cause its gonna look badarse when its completed.
hope this will help you run your chit,not scare you into getting rid of your equipment,that just sucks.

 

This is the first thing I thought ... alternator out ... so I pulled out .. I tried it and replaced the battery ... passed two times through the alternator and my battery is brand new .. I installed the alternator and still have the same problem ... The car was good and I will be out to go work in the morning and does not turn on .. I then had to jump out ... I want to run a 12 with my kenwood amp but I do not know until ... so it could be a possible wiring problem? .. I do not have dimming lights or buttons ..