I didn't use any of the original wiring, not sure if any of it would work with a different kit. The bluetooth kit I got came complete with looms, etc so just ran those in.
You don't need to remove the seat to get the old unit out, just slide it right back. You should see a cutout in the carpet near the front of the runner where you you can get access to it. If you are installing a whole new kit then just leave it in there as its easier! Has your kit got the cradle fitted above the glovebox? Mine had this which I also removed. You need a new glovebox for that.
The Skoda bluetooth kit I installed is fitted underneath the drivers seat but on top of the carpet.