Installing a aftermarket stereo on a 2001 maxima?

my maxima had the Bose system so when i installed the new HU i i hooked it using the preamp outputs on the headuint coz the speakers go thought the factory Bose amp it sounded fine same as the factory bose, but i need more trebel so what will happen if i hooked the speaker wires to the bose amp instead of the pre amp outs coz i recently installed 2 12" and the subs are overruling the speakers all i hear is b and not much throught the speakers the amp is a 2000W hifonics and 2 12" alpine x types