Deep Cycle Marine Batteries
To specifically answer your question. There are actually 2 circuits to be concerned with, and YES ever circuit should either be fused or have a breaker. You want the breaker to trip to shut things down and avoid a fire. Without a breaker or fuse if something fails, the wires will get hot and burn.
The one circuit is for the DC alternator and it comes from Minn Kota with the appropriate fuses. You can extend the cables. I mounted my DC Alternator under my console and the cables to the TM batteries were long enough to get to them. However the cable to the starting battery needed to be extended and I believe I had to use 10 gage per the instructions. Obviously I soldered all the connections and covered them with heat shrink.
The other circuit is your trolling motor circuit and YES it should have a breaker or fuse. The largest TMs draw more than 55 amps but less than 60, so that is why the guys use the 60 amp waterproof resettable breaker. (Amazon is the cheapest)
You should also make sure you kill the power to your TM when you are charging for any period of time. Most TMs have a circuit board in them and a voltage spike can take out the circuit board. Voltage spikes can happen for lots of reasons. I wired my TM in Series and mounted a shutoff switch under the console. The shutoff is on the connection between the + & - of the circuit. You can also unplug your TM but that will eventually wear out the plug.
I also have a master shutoff on my starting battery as this also kills the trim on the big motor. I saw a guy have a trim switch fail and the pump on the motor kept running with the motor all the way up, good thing the guy caught it and disconnected the battery or he would have burned up his rig.
So when I am done fishing I turn off both master switches and the power on my rig is 100% dead. Sure helps a guys sleep and I would never own a rig without them. You can also get the switches off Amazon for about $30 each.
So to properly wire a boat with the correct size marine wire, terminals, non-plumbing grade solder, fuses, and shutoff switches will probably cost $200 but when you look at the cost of the contents of a boat or even having a structure fire,,,,,that is cheap IMO.
I also agree, wire size is SO important. Don't assume what you need. Look it up on a chart (Amp Draw & Length of run) My Minn Kota 80 pound Terrova draws 56 amps on full (which we do use when muskie fishing into the wind). I also installed a master shutoff switch under my console on my TM circuit which I would recommend. The chart told me 4 gage. You also want to use Marine grade wire. I also upgraded my plug to a Battery Tender Plug which is rated for 100 amps. (I was smoking the factory ones that came with the boat)I also soldered all the connections. The circuit is only as good as the weakest link.
The age of your trolling motor plays a huge role in battery life as well. Newer motors are going to be more efficient. That 80lb Terrova doesn't use juice the way a 65lb PD did on the same boat.
I've installed a Minn-Kota DC Alternator and that thing is very nice to have. It charges my trolling motor batteries off of my gas outboard. Last year (first full year with that thing on board) I only plugged my regular on board charger in maybe 3 or 4 times. It's not a necessity but it's a neat toy to have. Trolling motor batteries get run down? No problem...just make a run or two across a lake and they are charged up enough to get you through the rest of the day.