If you go the sub only route, you'll use two of the four amp channels bridged to drive the sub. (See amp manual on brdiging). So half the amp is wasted I'm afraid!
The headunit will continue to drive all four (highpassed) standard door speakers.
To connect the amp, find the rear speaker wires under the sill cover, just before they go into the rear door.
Strip back 10mm of insulation from both wires of the pair and crimp or solder extension wires to reach the amp in the boot. Repeat on the other side of the car. Use the same colours each side to keep the polarity the same.
The original wires are driving the speakers, you just tee into them under the sill.
You should high pass the speakers, as you can drive them harder. Remember, if you have to turn the bass down to avoid distortion because of un-high passed speakers, you'll also be turning the sub bass down too.
Also, you must make sure the fader is set to provide enough output to the amp. (Fade to the front and the sub will fade out).
All this is of course assumes your amp has decent quality high level inputs! What model amp and sub are you using?