I say your stupid
YES, the alt - > batt positive goes straight form the alt, tot he battery + terminal, no runs through the fuse box or any of that bs. Fuse that line with an aftermarket holder if you wanna be careful, many (me included) dont use one
As for your grounds, shorter the better, try and ground to a more solid spot, like the shock tower bolts, sand the hell out of the paint to get to bare metal, no " oh thats probly good enough", take out the 60 grit and get some shiny metal showing!!!