I had the pro Nav NBT system with no amp and nothing in the boot apart from the Bluetooth module and diversity unit. As I did not want to dismantle the dash, I left well alone and lifted the carpet near the under-seat subs and cut the speaker wires there. The front door speakers are fed from the sub, so you can splice into them, and I also managed to find the rear door speakers under the carpet in the same area, which I also cut. So basically where I cut the speaker wires, I then extended them to the amp in the boot and connected to the high level inputs of the amp, I did this for the four channels. The amp then converts to six channels (low Hz for the subs) and I ran 4 new cables back to the under-floor sub area and connected into the wires going to each door, and I ran 2 new cables from the amp low frequency outputs direct to the subs.
I may be able to explain better with the following picture taken at the time from under the drivers seat. The larger pair of blue/red cables are from the head unit front driver side channel, this originally fed the sub which had an output going to the front doors for the original full range basic speaker - the smaller pair of blue/red cables are to the door. So I simply cut the connector off, extended the larger pair of blue/red to the boot for the new amp input and then a new cable back to join the smaller pair of red/blue cables to feed the front door speaker. The sub was then fed direct from the amp to the sub with the larger black/blue cable you see in the picture.
The finished result is then felt taped to stop rattles and the sub fitted. I had to crimp two spade connectors onto the sub feed as you can see, you can also see the original cables that I extended under the carpet. This is all you need to do on each side, then simply fit the door speakers.
This is the amp mounted in the boot.
Let me know if you need any more info, I can do a diagram if required.