I am going to completely remove the bose setup at some point and use the wiring thats in the car to run the door speakers from an amp and have another amp to run the 2 subs in the parcel shelf. I have a kenwood headunit to go in which is quite old now and i want to get focal component speakers for the doors. Should be able to use all existing wiring to get signal from headunit to the amps and from amps back to speakers in the doors. Just need to run new power cables for amps. Its going to be a nice little project when i have bought everything. 
Depending what Amp(s) you end up using, assuming the amps are going in the rear, your probably end up running some screened preamp cable aswell, as the Bose uses balanced cables at low speaker level between HU and Amp.
On the Subs, subject to room under the parcel shelf, you could fit bigger speakers than the Bose holes allow, in my company car days where we weren't allowed to make holes bigger, I quiet sucessfully fitted Base Speakers under the shelf by making chipboard baffles and spacers under the shelf, ie 10" speakers with a 6" shelf hole with very good results, as long as the Air Flow is tight between baffle and shelf and the Speaker movement area is free.
Edit: Just read, Daves already mentioned earlier about offering the speakers from underneath,
