The rear speakers have been discussed in anther thread most of us agree not to put anything there. Also I think you mean 2 way setup 1 way is just one speaker you have a tweeter and a woofer that is a 2 way. Yes you get a lot better sound from upgrading the head unit. No matter what you buy stock systems are nothing more than something there to play music. Even if it is the bose one it is not as good as what you paid for it could be.
Stock speakers vs aftermarket
As for the bose here is there sub amp now that thing can not push any sub hard. See the difference?