OK
1. You mount the cradle for the head-unit in the upper half of the cavity, most people are content with just jamming it in there (it a very tight fit at the best of times) and then using a snap in pocket for underneath. But to do it properly yes you should pop rivet the cradle in on each side, just use a cordless drill with the correct size bit and drill as close to a right angle as possible, a small angle wont affect anything.
2. Good place if it'll fit is on the back of the rear seat, if not then the next easiest place is on the underside of the parcel shelf. Mounting it on the sub box is fine, providing the amp is decent quality. Big downside to this is if you want to take the box out to make room in the boot, its not just a simple two wire disconnection from the speaker box terminal and then taping them up etc. You will need to disconnect the power / remote / earth wires along with the RCAs.
3. If you are just replacing the standard speakers with something like 2 or 3 ways then the stock speaker wiring will be OK, just use some spade terminals and speaker wire to adapt the plugs to the new speakers.