What does that have to with my suggestion to replace the hu and forget the cd changer? You bought speakers. Now finish it off with a $100 hu. A 40w per channel amp is about as useless as an anchor on your car; may as well re-sell or toss it. I stated my opinion...take it or leave it.
Here; I'll break it down for you.
1)of course it is
2)you bought the speakers...why not use them?
3)"the bose setup" is just speakers? If you want better sound, speakers alone won't cut it. DITCH THE BECKER UNIT! A cheap $100 pioneer head unit will outperform the stock unit and amp combined.
If you're not going to replace the hu, you won't be too impressed with the difference by only adding speakers.