99 Infiniti I30/Factory Bose help

If anyone out there thinks could contribute any amount of information that may help I would appreciate - Here is my situation:- I have just purchased this car, from my old car came Pioneer deh-6500/XM Skyfi/Rockford Fosgate 5100 2 channel/2 12" P2 Rockford Fosgate subs in sealed box/ - I did spend a considerable amount of money for these items so naturally I would like to integrete into my new car - Well here's the deal I am sure many people have come across the delema of upgrading your factory Bose to an aftermarket - Seems this is not at all an easy/reasonable thing to do, I have gone to my high end car audio store - where I got one story that included many parts and a HUGE estimate - then I travelled to Best Buy where I received a completely different story - I don't think I would let BB touch this car - I have a few questions that I hope someone can answer - - Would anyone out there recommend upgrading my factory audio? Take into consideration is does not at all even sound decent - One rear speaker sounds like it may be damaged - I love XM and would like to forget the skyfi and upgrade to XM direct - run right through my Pioneer deck - - Are there any recommened guides for upgrading factory Bose to an aftermarket system?