Wiring basics: can anyone help me out?

I'm wiring up my LS1 in my malibu and needed some basic wiring knowledge b/c its probably the weakest part of my automotive know how #-o .
The fact that I'm wiring up a fuel injected harness is irrelevant, its not that part that has me confused it just the basic stuff that I need help with. I have a remote mount battery in the trunk and just a regular starter and alternator system. I also have the harness fuse block along with the g-body fuse block that has all of my brakes/headlight wiring (the one under the drivers side dash) that I will need to tie into somehow.
Can anyone with some good wiring knowledge tell me where I should run what type (gauge) wire to what connector? The starter has 3 electrical hook ups, the alternator has just one post in addition to the usual plug in clip. The fuse block has 3 posts one of which still has a cut off ground strap left on from where I robbed the harness from a 99+ truck. I have diagrams for what relay/fuse to hook up my fuel pump and the ones for the "key on" "hot at all times".
Taking the car to someone is not an option b/c I'm short on $ and have pretty much no way of hauling the car, so any help on just basic starter/alternator/key switch systems would be greatly appreciated.

Let me rephrase everything to make my question seem simpler. If you had an old style carb/engine with a relocated battery box and had to wire everything up to where the engine would crank, how would you do it?