Alternator and big stereo help and curiosity...

I'm currently running four Deka 31 series batteries. I just got my hands on about 100' of 1/0 gauge Knukonceptz OFC wire which I'm gonna use to run to my two Zapco 750.2 amps that are running two WS Pro 485's and also to a Rockford T1500 powering two 12" Rockford subs. I plan on having a lot of wire left over and was wondering if it would benefit my charging system to run that big of a wire off my alternator and to also replace the 4 gauge wire connecting each battery together with the 1/0 gauge wire? My biggest concern is the wires off the alternator. Would I just replace the stock wiring off the alternator with the 1/0 gauge or should I run it additionally to the stock wiring? If I simply replace the stock wiring, do I need to add a fuse anywhere? Is there any possibility of harming anything electronic like the ECM or anything by adding the bigger wire? Thanks for any info.