Fuse are like a switch. If a fuse blows, the circuit opens and no current can flow. What happens when it/they blow depends on where they are in the circuit. First, there is no logic in installing two fuses back to back in a circuit so you first need to make certain that's the case. Exceptions to this would be in the case of a radio, locator or other sensitive electronics where the electronics themselves have a fuse. Typically the circuit feeding such a device would have a fuse at the fuse panel. That fuse protects the run of wire to the radio or electronics. The fuse at the electronics would be much smaller and would blow if the device circuitry malfunctioned. But since that means the device is likely "toast" anyway, that fuse is merely fire protection. Batteries, motors, lights, and such only require fuses at the circuit source (fuse panel). Most chargers have a fuse in the line between the charger and the battery. There would be no need to have two of them. In your case, there should also be a fuse in each of the 12 volt lines between the batteries and the trolling motor. This would account for four fuses, none of which are back to back. If a fuse in the charging line blows, the troller will still run but the associated battery will not be charged when the charger is plugged in. If a fuse blows in either of the lines between the batteries and the troller, the troller would likely stop running because the "series" connection to the motor would be broken. The batteries would however continue to be charged normally since those fuses are not associated with the charger.
