You should fuse the positive lead about 2"-3" away from the battery and fuse the negative, which should be short and going to the chassis in the trunk.

That rubber boot is exactly where I sent the 4AWG thru for my car. Ran it across the inside back of the dash, down the driver's side of the center console, under the carpets up behind the back seat and into the trunk. I think there was already a rubber grommet in the back seat wall for passing electrical wires to the trunk. Pretty easy job, actually. In my 1985 300DT. :-) Good luck.