Ok this diagram is naff coz it's drawn in paint but I will try to explain.
Not sure what your skill level is so i'll be basic, so sorry if i'm just telling you stuff you already know.
First of all make sure you have an amp wiring kit suitable for your amplifier.
Cut a length of your thick power wire (about 50cm) connect a battery terminal to one end and the fuse holder to the other end. The fuse holder should be as close to the battery as possible, NOT in the boot like i've seen some people do. The whole point of this fuse is so if you get a short on the system the fuse will blow and prevent your car from bursting in to flames. If your short is half way down the car and the fuse in the boot?? not very helpful.
Next, from the fuse holer run the wire down the drivers side of the car and into the boot (Assuming the sub is going on the right hand side, if not route accordingly). You will need to drill a hole under the engine bay to route the wire through. I found a rubber grommet in the centre of the bulkhead so drilled a hole next to it as my power wire is THICK. Just made sure you don't drill through cables, fine a nice single skinned panel to drill through.
Thats the hard part done. you now have a positive feed in the back of the car.
On the head unit you should have a blue wire (possibly labeled remote). Run this to the boot of the car also.
Fold the rear seats down and pull back the velcro carpet. There is a metal brace that goes across the car, at either end is a ncie shiny bolt which works well as an earth point, connect your black earth wire to here and route to your amp.
NOTE: whilst doing this work leave the positive wire disconnected from the battery.
ok, almost there. connect your power wire to the amp, along with the earth and the remote. All should be labeled up on the amp. I guess your sub is already wired to the amp but if not then connect these also.
The head unit should plug straight into the car if you get the correct audio lead from halfords or similar. You shouldn't have to worry about the in car speakers then.
Not sure if there is anything else to it really, it's a very straight forward setup.
Just tidy up all the wires by routing them under the trim and then finally plug in the fuse and connect to the battery.
If you need anymore detailed info then let me know and i'll take some photos.
Cheers, Matt.