Yes, you can replace the stock Bose am (which does suck) with another amp. If you don't change the speakers, make sure the amp can handle the 2 ohm load of the stock speakers.

What car do you have? The Bose amp takes the 4 channel input and splits it to 6 channels in the coupe (the 2 extra channels for for the 6x9 subs in the coupe) and 5 channels in the sedan (for a single sub) so if you don't add something for low bass, it will be lacking in the new setup.

 

I have a 03 Sedan and the amp will not work I was informed by installer dammit. Its 2 channel. The installer wanted to buy the amp from me. Its an older Linear Power. He collects older amps. I am keeping it though.

 

You could run 2 channels with it.