quality of aftermarket speakers on factory nav

im89

i have the bose system and it sounds pretty good to me. honestly i just wished it had some more bass. i dont want anything crazy , dont need my trunk shaking...any advice? i went to a shop and they said it would be better to take out all the speakers and put a whole new system because the quality would not be good on the factory nav. i actaully purchased a jl audio setup c650 components c2 350x for the rear and 12w3v3 but i planning to return because i didnt plan to get the bose system with the car.(got a really good price) i guess my main question is will it sound better than my bose system or will i have to get a new head unit to used these speakers to their full potential. i really like the factory nav. i just want a little more bass to my system.