Yes a fuse for each positive wire coming from the battery. The fuse is the only protection your wiring has. The fuse protects the wire, not the electronics. Having said that, you can replace the fuse for the wire with a fuse for the sonar unit as long as the fuse for the sonar unit is less than the one required for the wire. As stated above, most are 3 amp, however read your owners manual to be sure. I'm thinking I used 2 amp fuses for my core HB units.
As for the wiring runs. At minimum run the trolling motor wiring away from your electronics run.
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