Since a 24V, or a 36V, is a series circuit, the breaker can be put anywhere in the circuit, but close to the battery is best. The crossover is a good place for an inlne breaker. For the trolling motor to work after you took the breaker out, indicates a problem with either the breaker or the connection at the breaker. As you said, you were getting the voltage, but when loaded, the voltage and amps would fall and not run the trolling motor. I do hope you installed another breaker.JohnJones Trolling Motor Services870 773 3474Motorguide/MinnKota/PowerPole/Lowrance/Humminbird