The Orion DC to DC chargers can be activated either by a connection to the ignition switch or by measuring the vehicle battery voltage. If the vehicle battery voltage is above the voltage of a full battery it is being charged. If it drops below this the Orion shuts down. When connected to the ignition switch it only runs with the ignition on.
The best place is in trailer next to the batteries so there is no voltage drop on the output. If there is voltage drop on the input then the Orion can boost this. You will need to oversize the input wires to keep voltage drop low and fit good quality connectors. Many DC voltage drop calculators on line.
See link below vs isolated and non isolated. The choice depends on if you common ground the vehicle and trailer. You can use isolated in a non isolated situation but not the other way.