Upgrading Bose Premium (PLEASE HELP)

Well, recently my 2002 Oldsmobile Bravada that I fell in love with had to be laid to rest due to a careless driver who was texting and speeding... So I bought myself a 2005 Buick Rainier with Bose Premium Sound. In my Bravada, I had installed an amp, head unit, Infinity door speakers, and 15" Kicker CVR, so I'm not completely in the dark as far as audio goes, but I most certainly am no expert. Also, I'm not a basshead. I just want good quality, but with the extra volume, ability to listen to my iPod, and crisp sound that I grew so accustomed to with my beautiful Bravada. (RIP)

My first predicament that I have, however, is that my Bravada did not have Bose Premium, and I'm not very familiar with it, but plan on installing a sub, amp, and aftermarket head unit (Alpine Type-S 12", Boss 1000watt amp, JVC Arsenal KD-AHD79). I already have the amp and sub, but have yet to order the head unit. I know that I require a special harness, the CRUX SOOGM-15 GM Factory Integration Adapter,(correct me if I'm wrong) but that's all I know. So first off, does the Bose amp work with aftermarket head units, or will I be forced to run wire to each speaker to bypass the amp and run from the head unit? Will I still keep my EQ controls with the new head unit, or will the settings from the Bose head unit stay and leave me without control?

My second predicament is that I've heard so much about Bose speakers not being the top notch quality I've been lead to believe. Will the absence of the head unit diminish the quality of the speakers, whether or not I bypass the amp? As of right now, I do not plan to bypass the amp since I don't feel like running wire to all 6 speakers, but have been thinking about upgrading the door speakers if the quality will not be up to par with what I want. Will aftermarket speakers sound better, even with the Bose amp? The Bose speakers as they are seem like a good quality sound. If I do upgrade speakers, however, what sizes are the front and rear speakers, and what Ohm loads are they?

Finally, I did some research and some people claim that the front door speakers are in fact not speakers, but subs. I personally haven't taken anything apart yet, but have noticed that the front door speakers are the source of most of my bass. Is this because the speakers are actually subs not designed to take full range output, as a normal car stereo speaker is? If that is the case, then is the amp designed not to give these speakers any mid range or high range signal? I wonder, because if I install my 12" Alpine Type-S, which I plan to, I would want these speakers to be full range, as I wouldn't need them to hit the lows.

Sorry this is such a long thread topic for a newbie, but I'm trying to set up an excellent audio system in this car that I can enjoy on my hour long commute every day.

If anyone can answer my questions and/or give me their suggestions on how I should go about making my upgrades, I would greatly appreciate it since, as you can tell, I lack of knowledge as far as this goes.

Thank you!