Replacing stock stereo system

Hello everyone, I've taken a look over the site and I must say it is good to see so many people able to communicate over a great vehicle. I would also like to thank you for your time in reading this post.

I would first off like to get started by saying I have already replaced the stock head unit with a single din receiver, added an amplifier and two subwoofers. They have worked great so far, other then the fact that I lost my automatic start on the car, and I'm assuming this is to losing my factory head unite. If not I would love an answer for that. What I am doing is actually replacing the BOSE unit, putting in new speakers and a new amplifier. Due to my excessive loudness of almost any time of music, I have most certainly blown the back two 6x9's which I didn't actually plan on replacing. The only speakers I plan on truly replacing are the current 6 1/2" speakers in the doors, along with the tweeters. I am putting in a set of Apline SPR-60C's, and also plan on unhooking the middle speaker on the dash. I figured these speakers would easily outpower any of the BOSE speakers, and would sound great while doing it. I am mainly concerned of how to do this, would I no longer need the wiring harness which costs over $100 to use the BOSE unite? I remember having to have a special piece added due to that system for the car to function properly or something I can't remember, so I am hoping someone here could help me out a bit.

Thanks everyone

You should keep the center speaker on the dash, it wont hurt anything it will actually help bring the sound stage up and your music will sound better. If it inst broke dont hurt it lol.

On your question to the speakers...i have no answers sorry...but for your remote start issue...if you kept your head unite which i hope you did because i redid my whole system and if you dont keep it, it will throw codes and will make it so you can't see your little display computer there is a hook up for that, i have it running out in the trunk of my car, also i would have to say go with JL Audio TR's they are great speakers i have and i ran an amp(300/4) to them, also i have a 10' JL w7 with a 500watt sub running to that both amps JL audio...everyone that has heard it says by far one of the loudest single subs and cleanest systems. but thats just my 2 sense on the starter...