power wire/alt

cars with batteries in the trunk are the alt wire protected by fuse/breaker in case of accident or it gets pinch?
why i ask because i am upgrading alt wire dont know if i need to fuse it on the battery side or both sides of the run? or dont fuse my run because the stock wire will still be used and if the fuse pop of my run there is still a chance of the car catching on fire because of the stock alt wire not been protected

you just fuse on the battery side. you protect the battery from exploding in the event of a short. the alt output isn't protected from a short as it will just fail, not cause any fire hazards.