Definatly put the fuse under the hood, as close to the battery post as possible. The use of a fuse is to protect your equiptment (and your car) in case there is a short. If tge fuse is all the way in the trunk, then thats about 10 feet of wire that is unprotected, and could cause serious damage if there were problems.
I had similar problems with the lights dimming. Upgrading to a deepcycle battery (such as an optima) fixed it for me. Caps are a band-aid to the wound... upgraded grounds, good battery, and possibly an alternator (if yours is capoots) should fix your situation.
I hate caps... I think they are almost useless... (almost)
