Technically you can replace one or the other...but due to a difference in resistance, whether it be at the amplifier in the aftermarket radio, the factory bose speakers, the aftermarket speakers, or the factory bose amplifier...EVENTUALLY your system will take a **** on you because the factory bose amplifier outputs @ 8 ohms while aftermarket speakers are at 4 ohms...and obviously an aftermarket radio puts out its signal at 4 ohms.

Best bet in the long run is to replace everything and bypass the bose amplifier