The Marinco 12/24 plug/receptacle are pretty versatile, allow charging the 12V batteries via a single charger from a 12V jumpered plug, 12 or 24V trolling motors, I even run high power fishing lights off them. I have an I/O with a high amp alternator, and with the plugs I can charge the trolling batts while on the water, (takes hours)...
Yes breakers on each batteries positive connection, 60 amp if that's recommended. I'm using inexpensive 50 amp breakers on my 70# MK and haven't popped them, or noticed a lack of performance from the TM, $5 vs $30+. Be sure to use manual reset breakers - NOT automatic reset.
What TM was on the boat before, make, voltage and thrust? Is the wiring up to snuff (heavy enough) to run your new TM. Google "blue seas dc wire calculator", it will tell you what size of wire is needed by inputting: amps power draw, voltage and TOTAL length of wire runs (4). I use 3% voltage drop in the calculator.