personally what i would do:
get a new HU
get a 4 channel amp for the mids and highs
get a class D amp for the sub
get a sub
all the wiring and supporting to boot
run new wires to all the speakers from the 4ch amp thus totally bypassing the bose system (can be a real headache)
it will sound allot better and much more up-gradable also can go back to stock easy if you decide to sell