Good Question.
First off, it all depends on what kind of current your going to be drawing to tell you exactly what size wire, and batteries you are going to need, and alternator size as well.
My suggestion without knowing any of the equipment you are going to buy/use(unless its the stuff in your sig) is....
1. Buy a HO alt, preferably 140-160 amps or higher if you want.
2. Do the Big 3 with 1/0awg, make sure you fuse it with the correct fuse. If your alternator is 160 amps, get a 160 amp fuse and nothing less etc, 140-140 etc.
3. After you have a new alternator, and the Big 3 buy a Kinetic battery. You can buy other ones such as deka and northstar optima...whatever I go with Kinetics because they are cheaper, and you get more amps out of them.
EBay them and you should be straight.
4. RUn a 1/0 awg wire to the back of your car, so with doing the big 3 and the run to the back, id say you need about 25-30 feet or so.
Of the wiring, battery and alternator, Each work with one another. Just make sure you fuse correctly just incase you dont blow something up!
I hope I helped, I used to be really stupid at this stuff.