The top pic is two 12 volt battereis ran in series to get 24 volt. The bottom pic is two battereis in parallel that still gives 12 volts.
Use the top diagram with an inline circuit breaker rated for the amprage on your trolling motor. I ran 6 awg tinned copper wire for my 80 pound Minn Kota Terrova with a 60 amp inline breaker. The setup works great!!!!