heres me chiming in. Ive had several setups within a very short time. first off, i had just an ipod hooked up to the stock bose. Sounded good, but needed more bass, the stocks where very sub par.
Then I added the sub. I bought a 4 ch amp just because i knew i was going to upgrade eventually. Glad i did because the upgrade came sooner than i thought. Anyway, I went with 2-10" subs in the rear. I was pretty happy with this setup, until i noticed what i was missing when i ended up with components. Basically the subs were able to drown out the poor quality of the stock system.
Next I screwed up my headunit, so i went ahead and ordered an eclipse something.

i cant for the life of me remember right now. i'll get back to you on that one. Now to avoid having to have to get a ridiculously expensive adapter just to make the crappy bose speakers work. I borrowed a set of coaxial speakers from greg. These were a much improved sound over the bose. Much clearer, but you can tell something was missing. The mid bass was what was missing.
After this i went ahead and ordered a set of 6.5" 2way components. After about a month of tweeking. it took this long for me because i havent had an aftermarket HU in many many years and was basically back to square one with tuning. I finally found what was missing. Ive got the range pretty well covered. I will eventually move to 3ways, but this wont be for a few years. Other projects to take care of. I also got rid of the rear speakers.
When the rears were in, it seemed like there was too much going on behind me. Didnt like it at all. I got used to not having rear speakers very quickly. All I had to do was run another set of rcas to the amp and i was good to go. ran new wire for the speakers in the doors. I couldnt be happier. You may think that the bose sounds good enough, then you upgrade and you can start to hear what youve been missing. I hear so much more detail now. I still have to play around with the gains a bit, but im set for many years to come with this simple setup.