well when you add an aftermarket deck to the bose system, the internal amp of the radio isn't driving the speakers. the bose amp on the car is, unless you rewired the car and the now the radio is powering the speakers.
the noise you are taking about is probably alternator whine. in this case you might want to ground the headunit else were making sure to scrape away any paint. if that doesn't help, try a ground loop isolator. these work wonders.
as far as the bass issue is concerned it all comes down to personal perference.