After you find the reason for the shorting you could always use a self resetting circuit breaker - about $5 from any FLAPS, Boating outfitter, farm store, etc.
Or you could use fusible link available at any automotive store. It is a lead/tin based wire intended to burn out like a fuse. All Domestic automakers use this on all leads from the power tap to the fuse block on all vehicles from the mid 70's on. It is intended to blow at a higher value than the fuse, however it is intended to prevent fires (and have the service department charge you $2500 for a new harness vs $1 worth of fusible link)
However the original idea of running all the system current thru an ammeter worked well when the total system load was about 10 amps, however with a power plant swap, alternator swap, etc. the original wiring may soon be taxed. I myself am going with a simple volt meter.
For example todays cars 150 amp alternators, defrosters, heated seats, gazillion watt stereos, xenon headlamps, etc. the load center on todays cars is connected to the battery with a 4 gauge wire, sometimes with a 120 amp fuse, or more commonly with a splice and 10-20 circuits of fusible link.
