There's actually no need for a fuse near the DC/DC charger, which will not send power back up the line and should have a fuse on it for its output. If they're mounted in proximity to the battery you might consider not fusing near the battery but if something goes wrong, it's the battery in the back that will have the juice to cause problems not the DC/DC charger so you'd move the fuse (40A ought to be enough) to the line between the battery and the DC/DC charger.
Do you run a separate negative wire? Good question, some say no, some say yes. If you don't, then every joint between the DC/DC charger and the battery up front becomes a possible failure point. It becomes a matter of risk - do you take the risk, or go to the expense of removing the risk?