On mine I wrapped up the original + terminal and hid it. I ran the wire from battery to the starter since that's the highest amperage drawing thing on the car. The original wire that fed the starter now supplies the battery current to the fusebox via the hidden terminal that still has all wires attached. In the trunk I used a marine fuse holder and fuse. Much better than the flashy fuse holders like most stereo shops use.
Fuses are available up to 800amps for these. I'm using a 150a.
I used a 4awg wire to run to the starter and used another to ground the battery to the speaker tray below the rear window. I've been using this setup for 3 years or better with no charging problems or any other issues. My battery is vented out of the trunk also.