Best way to mount it and save the boot is on the side behind the wheel arch, but unless you do it yourself it costs a lot. Lewy's installs like this and is sweet!
But for simplicity I'd go with Dizzie, mount a sub in one corner of the boot with some plugs on it so you can take it out easily. Run power wires down the passenger side of the car and speaker wires along the middle, all under the carpets.
Rear speakers in the parcel shelf are a bit of a no no when you have a sub in there as the sub's motion will restrict the movement of the back speakers cones. Get some decent components up front instead, mounting the bass in the door and the tweeter in the dash.
Have a check on
http://www.caraudiodirect.co.uk/ for some decent cheap stuff!