Which end do you fuse? Both the battery and the alternator can supply power. I would assume the rectifier in the alternator would fry, thus acting like a fuse..but what if it didn't?
usually the main power wire is fused at the fuse box, yeah. as for which end, it should be on the battery end for the exact reason you just stated. the alternator has a little bit of built in protection, but the battery doesn't in case of a short.