Yes you can do all of that with the factory head unit. Is it recommended for what you asking...no. If you want the best possible sound then you should use an aftermarket head unit.
To keep the stock head unit you will need to an aftermarket adaptor. Like the sven4
http://peripheralelectronics.com/web/loc.asp
You will need to run new speaker wires.
Personally I do not use the rear speaker locations. They are too close to the drivers head. The door will house both 6.5" drivers if you are looking for max volume. If you use a front and rear on the same channel you will not be able to fade front to rear. But your amp will not have a problem driving two sets of speakers. The sub on the mono channel will be fine.
As for amp location there are not alot of options. Most people put it on the luggage tray in the hatch. You can mount behind one of the seats but then it limits the amount of rear travel distance the seat has.